Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs16863886

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:222567378 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.309570 (81940/264690, TOPMED)
C=0.307395 (43074/140126, GnomAD)
C=0.26767 (7908/29544, ALFA) (+ 19 more)
C=0.06699 (1893/28256, 14KJPN)
C=0.06593 (1105/16760, 8.3KJPN)
C=0.3018 (1933/6404, 1000G_30x)
C=0.2987 (1496/5008, 1000G)
C=0.2696 (1208/4480, Estonian)
C=0.3160 (1218/3854, ALSPAC)
C=0.3290 (1220/3708, TWINSUK)
C=0.0791 (231/2922, KOREAN)
C=0.3096 (543/1754, HapMap)
C=0.344 (343/998, GoNL)
C=0.115 (91/790, PRJEB37584)
C=0.340 (213/626, Chileans)
C=0.282 (169/600, NorthernSweden)
T=0.395 (98/248, SGDP_PRJ)
C=0.421 (91/216, Qatari)
C=0.162 (35/216, Vietnamese)
T=0.49 (38/78, Ancient Sardinia)
C=0.40 (16/40, GENOME_DK)
T=0.47 (14/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FARSB : Non Coding Transcript Variant
Publications
1 citation
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 29544 T=0.73233 A=0.00000, C=0.26767 0.551246 0.086583 0.362172 32
European Sub 23844 T=0.71678 A=0.00000, C=0.28322 0.526506 0.092937 0.380557 25
African Sub 2736 T=0.8388 A=0.0000, C=0.1612 0.717105 0.039474 0.243421 8
African Others Sub 104 T=0.808 A=0.000, C=0.192 0.673077 0.057692 0.269231 1
African American Sub 2632 T=0.8400 A=0.0000, C=0.1600 0.718845 0.038754 0.242401 7
Asian Sub 144 T=0.965 A=0.000, C=0.035 0.930556 0.0 0.069444 0
East Asian Sub 94 T=0.97 A=0.00, C=0.03 0.93617 0.0 0.06383 0
Other Asian Sub 50 T=0.96 A=0.00, C=0.04 0.92 0.0 0.08 0
Latin American 1 Sub 150 T=0.793 A=0.000, C=0.207 0.653333 0.066667 0.28 1
Latin American 2 Sub 568 T=0.877 A=0.000, C=0.123 0.792254 0.038732 0.169014 8
South Asian Sub 64 T=0.78 A=0.00, C=0.22 0.59375 0.03125 0.375 0
Other Sub 2038 T=0.7085 A=0.0000, C=0.2915 0.515211 0.098135 0.386654 3


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 T=0.690430 C=0.309570
gnomAD - Genomes Global Study-wide 140126 T=0.692605 C=0.307395
gnomAD - Genomes European Sub 75894 T=0.67639 C=0.32361
gnomAD - Genomes African Sub 41986 T=0.72257 C=0.27743
gnomAD - Genomes American Sub 13646 T=0.68921 C=0.31079
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.5502 C=0.4498
gnomAD - Genomes East Asian Sub 3128 T=0.8664 C=0.1336
gnomAD - Genomes Other Sub 2148 T=0.6685 C=0.3315
Allele Frequency Aggregator Total Global 29544 T=0.73233 A=0.00000, C=0.26767
Allele Frequency Aggregator European Sub 23844 T=0.71678 A=0.00000, C=0.28322
Allele Frequency Aggregator African Sub 2736 T=0.8388 A=0.0000, C=0.1612
Allele Frequency Aggregator Other Sub 2038 T=0.7085 A=0.0000, C=0.2915
Allele Frequency Aggregator Latin American 2 Sub 568 T=0.877 A=0.000, C=0.123
Allele Frequency Aggregator Latin American 1 Sub 150 T=0.793 A=0.000, C=0.207
Allele Frequency Aggregator Asian Sub 144 T=0.965 A=0.000, C=0.035
Allele Frequency Aggregator South Asian Sub 64 T=0.78 A=0.00, C=0.22
14KJPN JAPANESE Study-wide 28256 T=0.93301 C=0.06699
8.3KJPN JAPANESE Study-wide 16760 T=0.93407 C=0.06593
1000Genomes_30x Global Study-wide 6404 T=0.6982 C=0.3018
1000Genomes_30x African Sub 1786 T=0.7178 C=0.2822
1000Genomes_30x Europe Sub 1266 T=0.6367 C=0.3633
1000Genomes_30x South Asian Sub 1202 T=0.5374 C=0.4626
1000Genomes_30x East Asian Sub 1170 T=0.8923 C=0.1077
1000Genomes_30x American Sub 980 T=0.707 C=0.293
1000Genomes Global Study-wide 5008 T=0.7013 C=0.2987
1000Genomes African Sub 1322 T=0.7216 C=0.2784
1000Genomes East Asian Sub 1008 T=0.8909 C=0.1091
1000Genomes Europe Sub 1006 T=0.6421 C=0.3579
1000Genomes South Asian Sub 978 T=0.533 C=0.467
1000Genomes American Sub 694 T=0.710 C=0.290
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.7304 C=0.2696
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.6840 C=0.3160
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.6710 C=0.3290
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9209 C=0.0791
HapMap Global Study-wide 1754 T=0.6904 C=0.3096
HapMap African Sub 682 T=0.677 C=0.323
HapMap American Sub 648 T=0.664 C=0.336
HapMap Asian Sub 250 T=0.884 C=0.116
HapMap Europe Sub 174 T=0.563 C=0.437
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.656 C=0.344
CNV burdens in cranial meningiomas Global Study-wide 790 T=0.885 C=0.115
CNV burdens in cranial meningiomas CRM Sub 790 T=0.885 C=0.115
Chileans Chilean Study-wide 626 T=0.660 C=0.340
Northern Sweden ACPOP Study-wide 600 T=0.718 C=0.282
SGDP_PRJ Global Study-wide 248 T=0.395 C=0.605
Qatari Global Study-wide 216 T=0.579 C=0.421
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.838 C=0.162
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 78 T=0.49 C=0.51
The Danish reference pan genome Danish Study-wide 40 T=0.60 C=0.40
Siberian Global Study-wide 30 T=0.47 C=0.53
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 2 NC_000002.12:g.222567378T>A
GRCh38.p14 chr 2 NC_000002.12:g.222567378T>C
GRCh37.p13 chr 2 NC_000002.11:g.223432097T>A
GRCh37.p13 chr 2 NC_000002.11:g.223432097T>C
Gene: FARSB, phenylalanyl-tRNA synthetase subunit beta (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FARSB transcript variant 1 NM_005687.5:c.*4493= N/A 3 Prime UTR Variant
FARSB transcript variant 2 NR_130154.2:n.6478A>T N/A Non Coding Transcript Variant
FARSB transcript variant 2 NR_130154.2:n.6478A>G N/A Non Coding Transcript Variant
FARSB transcript variant X1 XM_006712169.3:c.*4493= N/A 3 Prime UTR Variant
FARSB transcript variant X2 XM_011510466.3:c.*4493= N/A 3 Prime UTR Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= A C
GRCh38.p14 chr 2 NC_000002.12:g.222567378= NC_000002.12:g.222567378T>A NC_000002.12:g.222567378T>C
GRCh37.p13 chr 2 NC_000002.11:g.223432097= NC_000002.11:g.223432097T>A NC_000002.11:g.223432097T>C
FARSB transcript variant 1 NM_005687.5:c.*4493= NM_005687.5:c.*4493A>T NM_005687.5:c.*4493A>G
FARSB transcript variant X1 XM_006712169.3:c.*4493= XM_006712169.3:c.*4493A>T XM_006712169.3:c.*4493A>G
FARSB transcript variant X2 XM_011510466.3:c.*4493= XM_011510466.3:c.*4493A>T XM_011510466.3:c.*4493A>G
FARSB transcript variant 2 NR_130154.2:n.6478= NR_130154.2:n.6478A>T NR_130154.2:n.6478A>G
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

87 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23325989 Sep 20, 2004 (123)
2 ABI ss44331264 Mar 14, 2006 (126)
3 AFFY ss66524202 Nov 29, 2006 (127)
4 AFFY ss76346836 Dec 08, 2007 (130)
5 KRIBB_YJKIM ss83073376 Dec 14, 2007 (130)
6 BCMHGSC_JDW ss91561365 Mar 24, 2008 (129)
7 HUMANGENOME_JCVI ss97125328 Feb 05, 2009 (130)
8 1000GENOMES ss110827550 Jan 25, 2009 (130)
9 1000GENOMES ss111711308 Jan 25, 2009 (130)
10 ILLUMINA-UK ss118093597 Feb 14, 2009 (130)
11 ENSEMBL ss138637549 Dec 01, 2009 (131)
12 ENSEMBL ss142578734 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss165559678 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss165927123 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss167584662 Jul 04, 2010 (132)
16 AFFY ss173338344 Jul 04, 2010 (132)
17 BUSHMAN ss201791780 Jul 04, 2010 (132)
18 1000GENOMES ss219835774 Jul 14, 2010 (132)
19 1000GENOMES ss231602367 Jul 14, 2010 (132)
20 1000GENOMES ss239057831 Jul 15, 2010 (132)
21 BL ss253896516 May 09, 2011 (134)
22 GMI ss276913185 May 04, 2012 (137)
23 GMI ss284548906 Apr 25, 2013 (138)
24 PJP ss292495627 May 09, 2011 (134)
25 ILLUMINA ss479501801 May 04, 2012 (137)
26 ILLUMINA ss484021214 May 04, 2012 (137)
27 ILLUMINA ss533041879 Sep 08, 2015 (146)
28 TISHKOFF ss556249163 Apr 25, 2013 (138)
29 SSMP ss649912518 Apr 25, 2013 (138)
30 ILLUMINA ss779598529 Aug 21, 2014 (142)
31 ILLUMINA ss780997311 Aug 21, 2014 (142)
32 ILLUMINA ss835070482 Aug 21, 2014 (142)
33 EVA-GONL ss978002786 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1069972572 Aug 21, 2014 (142)
35 1000GENOMES ss1301811554 Aug 21, 2014 (142)
36 DDI ss1428923787 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1579339499 Apr 01, 2015 (144)
38 EVA_DECODE ss1587459308 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1605883476 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1648877509 Apr 01, 2015 (144)
41 EVA_SVP ss1712534048 Apr 01, 2015 (144)
42 HAMMER_LAB ss1798427790 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1921248282 Feb 12, 2016 (147)
44 GENOMED ss1969035630 Jul 19, 2016 (147)
45 JJLAB ss2021172229 Sep 14, 2016 (149)
46 USC_VALOUEV ss2149235618 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2239500187 Dec 20, 2016 (150)
48 ILLUMINA ss2633745143 Nov 08, 2017 (151)
49 GRF ss2703885212 Nov 08, 2017 (151)
50 GNOMAD ss2786799147 Nov 08, 2017 (151)
51 SWEGEN ss2991424235 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3024344480 Nov 08, 2017 (151)
53 CSHL ss3344759519 Nov 08, 2017 (151)
54 ILLUMINA ss3628296368 Oct 11, 2018 (152)
55 ILLUMINA ss3631704823 Oct 11, 2018 (152)
56 ILLUMINA ss3642157686 Oct 11, 2018 (152)
57 URBANLAB ss3647284412 Oct 11, 2018 (152)
58 EGCUT_WGS ss3659321624 Jul 13, 2019 (153)
59 EVA_DECODE ss3706104417 Jul 13, 2019 (153)
60 ACPOP ss3729407546 Jul 13, 2019 (153)
61 EVA ss3758135030 Jul 13, 2019 (153)
62 PACBIO ss3784165682 Jul 13, 2019 (153)
63 PACBIO ss3789702020 Jul 13, 2019 (153)
64 PACBIO ss3794575236 Jul 13, 2019 (153)
65 KHV_HUMAN_GENOMES ss3802497600 Jul 13, 2019 (153)
66 EVA ss3827526851 Apr 25, 2020 (154)
67 EVA ss3837182934 Apr 25, 2020 (154)
68 EVA ss3842605016 Apr 25, 2020 (154)
69 SGDP_PRJ ss3854681104 Apr 25, 2020 (154)
70 KRGDB ss3900408862 Apr 25, 2020 (154)
71 EVA ss3984498600 Apr 26, 2021 (155)
72 EVA ss3984956432 Apr 26, 2021 (155)
73 TOPMED ss4546092907 Apr 26, 2021 (155)
74 TOMMO_GENOMICS ss5156684084 Apr 26, 2021 (155)
75 1000G_HIGH_COVERAGE ss5252176424 Oct 12, 2022 (156)
76 EVA ss5314811432 Oct 12, 2022 (156)
77 EVA ss5336307468 Oct 12, 2022 (156)
78 HUGCELL_USP ss5451774700 Oct 12, 2022 (156)
79 EVA ss5506809304 Oct 12, 2022 (156)
80 1000G_HIGH_COVERAGE ss5529598814 Oct 12, 2022 (156)
81 SANFORD_IMAGENETICS ss5631034547 Oct 12, 2022 (156)
82 TOMMO_GENOMICS ss5687623016 Oct 12, 2022 (156)
83 YY_MCH ss5803255921 Oct 12, 2022 (156)
84 EVA ss5821648221 Oct 12, 2022 (156)
85 EVA ss5852968104 Oct 12, 2022 (156)
86 EVA ss5934875588 Oct 12, 2022 (156)
87 EVA ss5957294338 Oct 12, 2022 (156)
88 1000Genomes NC_000002.11 - 223432097 Oct 11, 2018 (152)
89 1000Genomes_30x NC_000002.12 - 222567378 Oct 12, 2022 (156)
90 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 223432097 Oct 11, 2018 (152)
91 Chileans NC_000002.11 - 223432097 Apr 25, 2020 (154)
92 Genetic variation in the Estonian population NC_000002.11 - 223432097 Oct 11, 2018 (152)
93 The Danish reference pan genome NC_000002.11 - 223432097 Apr 25, 2020 (154)
94 gnomAD - Genomes NC_000002.12 - 222567378 Apr 26, 2021 (155)
95 Genome of the Netherlands Release 5 NC_000002.11 - 223432097 Apr 25, 2020 (154)
96 HapMap NC_000002.12 - 222567378 Apr 25, 2020 (154)
97 KOREAN population from KRGDB NC_000002.11 - 223432097 Apr 25, 2020 (154)
98 Northern Sweden NC_000002.11 - 223432097 Jul 13, 2019 (153)
99 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000002.11 - 223432097 Apr 26, 2021 (155)
100 CNV burdens in cranial meningiomas NC_000002.11 - 223432097 Apr 26, 2021 (155)
101 Qatari NC_000002.11 - 223432097 Apr 25, 2020 (154)
102 SGDP_PRJ NC_000002.11 - 223432097 Apr 25, 2020 (154)
103 Siberian NC_000002.11 - 223432097 Apr 25, 2020 (154)
104 8.3KJPN NC_000002.11 - 223432097 Apr 26, 2021 (155)
105 14KJPN NC_000002.12 - 222567378 Oct 12, 2022 (156)
106 TopMed NC_000002.12 - 222567378 Apr 26, 2021 (155)
107 UK 10K study - Twins NC_000002.11 - 223432097 Oct 11, 2018 (152)
108 A Vietnamese Genetic Variation Database NC_000002.11 - 223432097 Jul 13, 2019 (153)
109 ALFA NC_000002.12 - 222567378 Apr 26, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs56454465 May 25, 2008 (130)
rs57018974 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
9973820104 NC_000002.12:222567377:T:A NC_000002.12:222567377:T:A (self)
ss91561365, ss110827550, ss111711308, ss118093597, ss165559678, ss165927123, ss167584662, ss201791780, ss253896516, ss276913185, ss284548906, ss292495627, ss484021214, ss1587459308, ss1712534048 NC_000002.10:223140340:T:C NC_000002.12:222567377:T:C (self)
12922771, 7150506, 243920, 5059872, 5504438, 3133922, 7586256, 2692411, 182359, 47937, 3290212, 6698084, 1751972, 14653391, 7150506, 1553440, ss219835774, ss231602367, ss239057831, ss479501801, ss533041879, ss556249163, ss649912518, ss779598529, ss780997311, ss835070482, ss978002786, ss1069972572, ss1301811554, ss1428923787, ss1579339499, ss1605883476, ss1648877509, ss1798427790, ss1921248282, ss1969035630, ss2021172229, ss2149235618, ss2633745143, ss2703885212, ss2786799147, ss2991424235, ss3344759519, ss3628296368, ss3631704823, ss3642157686, ss3659321624, ss3729407546, ss3758135030, ss3784165682, ss3789702020, ss3794575236, ss3827526851, ss3837182934, ss3854681104, ss3900408862, ss3984498600, ss3984956432, ss5156684084, ss5314811432, ss5336307468, ss5506809304, ss5631034547, ss5821648221, ss5957294338 NC_000002.11:223432096:T:C NC_000002.12:222567377:T:C (self)
17124749, 92131124, 2019725, 21460120, 349915786, 9973820104, ss2239500187, ss3024344480, ss3647284412, ss3706104417, ss3802497600, ss3842605016, ss4546092907, ss5252176424, ss5451774700, ss5529598814, ss5687623016, ss5803255921, ss5852968104, ss5934875588 NC_000002.12:222567377:T:C NC_000002.12:222567377:T:C (self)
ss23325989, ss44331264, ss66524202, ss76346836, ss83073376, ss97125328, ss138637549, ss142578734, ss173338344 NT_005403.17:73641514:T:C NC_000002.12:222567377:T:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs16863886
PMID Title Author Year Journal
21596488 Use of germline polymorphisms in predicting concurrent chemoradiotherapy response in esophageal cancer. Chen PC et al. 2012 International journal of radiation oncology, biology, physics
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post820+afb47a3d