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

Examples: rs268, BRCA1 and more Advanced search

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.

rs12714401

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:272840 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.410367 (108620/264690, TOPMED)
G=0.386354 (54095/140014, GnomAD)
G=0.17613 (4977/28258, 14KJPN) (+ 16 more)
G=0.36052 (7635/21178, ALFA)
G=0.17816 (2986/16760, 8.3KJPN)
G=0.4132 (2646/6404, 1000G_30x)
G=0.4018 (2012/5008, 1000G)
G=0.2719 (1218/4480, Estonian)
G=0.3171 (1222/3854, ALSPAC)
G=0.3182 (1180/3708, TWINSUK)
G=0.1980 (580/2930, KOREAN)
G=0.4165 (783/1880, HapMap)
G=0.286 (285/998, GoNL)
G=0.233 (140/600, NorthernSweden)
G=0.284 (131/462, SGDP_PRJ)
G=0.463 (100/216, Qatari)
G=0.136 (29/214, Vietnamese)
G=0.29 (14/48, Siberian)
G=0.35 (14/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ACP1 : Intron Variant
Publications
0 citations
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 21178 G=0.36052 A=0.63948, T=0.00000 0.141845 0.420814 0.437341 15
European Sub 15350 G=0.30482 A=0.69518, T=0.00000 0.092378 0.482736 0.424886 0
African Sub 3760 G=0.5543 A=0.4457, T=0.0000 0.322872 0.214362 0.462766 5
African Others Sub 132 G=0.515 A=0.485, T=0.000 0.30303 0.272727 0.424242 1
African American Sub 3628 G=0.5557 A=0.4443, T=0.0000 0.323594 0.212238 0.464168 4
Asian Sub 124 G=0.145 A=0.855, T=0.000 0.016129 0.725806 0.258065 0
East Asian Sub 96 G=0.12 A=0.88, T=0.00 0.0 0.75 0.25 1
Other Asian Sub 28 G=0.21 A=0.79, T=0.00 0.071429 0.642857 0.285714 0
Latin American 1 Sub 168 G=0.500 A=0.500, T=0.000 0.238095 0.238095 0.52381 0
Latin American 2 Sub 670 G=0.497 A=0.503, T=0.000 0.250746 0.256716 0.492537 0
South Asian Sub 98 G=0.50 A=0.50, T=0.00 0.244898 0.244898 0.510204 0
Other Sub 1008 G=0.3849 A=0.6151, T=0.0000 0.136905 0.367063 0.496032 1


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 G=0.410367 A=0.589633
gnomAD - Genomes Global Study-wide 140014 G=0.386354 A=0.613646
gnomAD - Genomes European Sub 75870 G=0.29895 A=0.70105
gnomAD - Genomes African Sub 41912 G=0.53130 A=0.46870
gnomAD - Genomes American Sub 13632 G=0.46956 A=0.53044
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.4016 A=0.5984
gnomAD - Genomes East Asian Sub 3130 G=0.1652 A=0.8348
gnomAD - Genomes Other Sub 2148 G=0.4162 A=0.5838
14KJPN JAPANESE Study-wide 28258 G=0.17613 A=0.82387
Allele Frequency Aggregator Total Global 21178 G=0.36052 A=0.63948, T=0.00000
Allele Frequency Aggregator European Sub 15350 G=0.30482 A=0.69518, T=0.00000
Allele Frequency Aggregator African Sub 3760 G=0.5543 A=0.4457, T=0.0000
Allele Frequency Aggregator Other Sub 1008 G=0.3849 A=0.6151, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 670 G=0.497 A=0.503, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 168 G=0.500 A=0.500, T=0.000
Allele Frequency Aggregator Asian Sub 124 G=0.145 A=0.855, T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.50 A=0.50, T=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.17816 A=0.82184
1000Genomes_30x Global Study-wide 6404 G=0.4132 A=0.5868
1000Genomes_30x African Sub 1786 G=0.5666 A=0.4334
1000Genomes_30x Europe Sub 1266 G=0.3104 A=0.6896
1000Genomes_30x South Asian Sub 1202 G=0.4451 A=0.5549
1000Genomes_30x East Asian Sub 1170 G=0.1744 A=0.8256
1000Genomes_30x American Sub 980 G=0.512 A=0.488
1000Genomes Global Study-wide 5008 G=0.4018 A=0.5982
1000Genomes African Sub 1322 G=0.5620 A=0.4380
1000Genomes East Asian Sub 1008 G=0.1687 A=0.8313
1000Genomes Europe Sub 1006 G=0.3121 A=0.6879
1000Genomes South Asian Sub 978 G=0.446 A=0.554
1000Genomes American Sub 694 G=0.503 A=0.497
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.2719 A=0.7281
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.3171 A=0.6829
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.3182 A=0.6818
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.1980 A=0.8020, C=0.0000
HapMap Global Study-wide 1880 G=0.4165 A=0.5835
HapMap American Sub 764 G=0.356 A=0.644
HapMap African Sub 688 G=0.594 A=0.406
HapMap Asian Sub 254 G=0.150 A=0.850
HapMap Europe Sub 174 G=0.368 A=0.632
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.286 A=0.714
Northern Sweden ACPOP Study-wide 600 G=0.233 A=0.767
SGDP_PRJ Global Study-wide 462 G=0.284 A=0.716
Qatari Global Study-wide 216 G=0.463 A=0.537
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.136 A=0.864
Siberian Global Study-wide 48 G=0.29 A=0.71
The Danish reference pan genome Danish Study-wide 40 G=0.35 A=0.65
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.272840G>A
GRCh38.p14 chr 2 NC_000002.12:g.272840G>C
GRCh38.p14 chr 2 NC_000002.12:g.272840G>T
GRCh37.p13 chr 2 NC_000002.11:g.272840G>A
GRCh37.p13 chr 2 NC_000002.11:g.272840G>C
GRCh37.p13 chr 2 NC_000002.11:g.272840G>T
ACP1 RefSeqGene NG_012035.1:g.12972G>A
ACP1 RefSeqGene NG_012035.1:g.12972G>C
ACP1 RefSeqGene NG_012035.1:g.12972G>T
Gene: ACP1, acid phosphatase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ACP1 transcript variant 3 NM_004300.4:c.231+690G>A N/A Intron Variant
ACP1 transcript variant 2 NM_007099.4:c.231+535G>A N/A Intron Variant
ACP1 transcript variant 4 NM_001040649.3:c. N/A Genic Downstream Transcript Variant
ACP1 transcript variant 1 NR_024080.2:n. N/A Intron 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 G= A C T
GRCh38.p14 chr 2 NC_000002.12:g.272840= NC_000002.12:g.272840G>A NC_000002.12:g.272840G>C NC_000002.12:g.272840G>T
GRCh37.p13 chr 2 NC_000002.11:g.272840= NC_000002.11:g.272840G>A NC_000002.11:g.272840G>C NC_000002.11:g.272840G>T
ACP1 RefSeqGene NG_012035.1:g.12972= NG_012035.1:g.12972G>A NG_012035.1:g.12972G>C NG_012035.1:g.12972G>T
ACP1 transcript variant 3 NM_004300.3:c.231+690= NM_004300.3:c.231+690G>A NM_004300.3:c.231+690G>C NM_004300.3:c.231+690G>T
ACP1 transcript variant 3 NM_004300.4:c.231+690= NM_004300.4:c.231+690G>A NM_004300.4:c.231+690G>C NM_004300.4:c.231+690G>T
ACP1 transcript variant 2 NM_007099.3:c.231+535= NM_007099.3:c.231+535G>A NM_007099.3:c.231+535G>C NM_007099.3:c.231+535G>T
ACP1 transcript variant 2 NM_007099.4:c.231+535= NM_007099.4:c.231+535G>A NM_007099.4:c.231+535G>C NM_007099.4:c.231+535G>T
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#.

86 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss21751386 Apr 05, 2004 (121)
2 WUGSC_SSAHASNP ss23110780 Apr 05, 2004 (121)
3 ILLUMINA ss65745944 Oct 16, 2006 (127)
4 ILLUMINA ss74875785 Dec 07, 2007 (129)
5 HGSV ss85161941 Dec 14, 2007 (130)
6 BCMHGSC_JDW ss91024107 Mar 24, 2008 (129)
7 HUMANGENOME_JCVI ss96369845 Feb 04, 2009 (130)
8 BGI ss106062968 Feb 04, 2009 (130)
9 1000GENOMES ss109147744 Jan 23, 2009 (130)
10 ILLUMINA-UK ss117555793 Feb 14, 2009 (130)
11 KRIBB_YJKIM ss119808197 Dec 01, 2009 (131)
12 ENSEMBL ss135913181 Dec 01, 2009 (131)
13 ENSEMBL ss138373948 Dec 01, 2009 (131)
14 GMI ss156584402 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss162983273 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss163709400 Jul 04, 2010 (132)
17 ILLUMINA ss172231186 Jul 04, 2010 (132)
18 BUSHMAN ss199925355 Jul 04, 2010 (132)
19 1000GENOMES ss210797466 Jul 14, 2010 (132)
20 1000GENOMES ss219014275 Jul 14, 2010 (132)
21 1000GENOMES ss231001266 Jul 14, 2010 (132)
22 1000GENOMES ss238594740 Jul 15, 2010 (132)
23 GMI ss276317459 May 04, 2012 (137)
24 GMI ss284274179 Apr 25, 2013 (138)
25 PJP ss292250660 May 09, 2011 (134)
26 ILLUMINA ss536810470 Sep 08, 2015 (146)
27 SSMP ss648873874 Apr 25, 2013 (138)
28 EVA-GONL ss976398782 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1068792278 Aug 21, 2014 (142)
30 1000GENOMES ss1295582438 Aug 21, 2014 (142)
31 DDI ss1428451286 Apr 01, 2015 (144)
32 EVA_GENOME_DK ss1578701964 Apr 01, 2015 (144)
33 EVA_DECODE ss1585800139 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1602630786 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1645624819 Apr 01, 2015 (144)
36 EVA_SVP ss1712424571 Apr 01, 2015 (144)
37 WEILL_CORNELL_DGM ss1919625826 Feb 12, 2016 (147)
38 GENOMED ss1968672834 Jul 19, 2016 (147)
39 JJLAB ss2020340171 Sep 14, 2016 (149)
40 USC_VALOUEV ss2148379511 Dec 20, 2016 (150)
41 HUMAN_LONGEVITY ss2226850179 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2624684676 Nov 08, 2017 (151)
43 GRF ss2702931422 Nov 08, 2017 (151)
44 GNOMAD ss2768836856 Nov 08, 2017 (151)
45 SWEGEN ss2988844662 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3023933380 Nov 08, 2017 (151)
47 CSHL ss3344030882 Nov 08, 2017 (151)
48 ILLUMINA ss3627972361 Oct 11, 2018 (152)
49 ILLUMINA ss3638237703 Oct 11, 2018 (152)
50 ILLUMINA ss3643209619 Oct 11, 2018 (152)
51 URBANLAB ss3646946600 Oct 11, 2018 (152)
52 EGCUT_WGS ss3656794744 Jul 12, 2019 (153)
53 EVA_DECODE ss3703087399 Jul 12, 2019 (153)
54 ACPOP ss3728077629 Jul 12, 2019 (153)
55 EVA ss3756248027 Jul 12, 2019 (153)
56 PACBIO ss3783756057 Jul 12, 2019 (153)
57 PACBIO ss3789358830 Jul 12, 2019 (153)
58 PACBIO ss3794231480 Jul 12, 2019 (153)
59 KHV_HUMAN_GENOMES ss3800636576 Jul 12, 2019 (153)
60 EVA ss3825593457 Apr 25, 2020 (154)
61 EVA ss3826773108 Apr 25, 2020 (154)
62 EVA ss3836791223 Apr 25, 2020 (154)
63 EVA ss3842204701 Apr 25, 2020 (154)
64 SGDP_PRJ ss3851407187 Apr 25, 2020 (154)
65 KRGDB ss3896775269 Apr 25, 2020 (154)
66 FSA-LAB ss3984166889 Apr 25, 2021 (155)
67 FSA-LAB ss3984166890 Apr 25, 2021 (155)
68 EVA ss3986168732 Apr 25, 2021 (155)
69 EVA ss4016975354 Apr 25, 2021 (155)
70 TOPMED ss4491522664 Apr 25, 2021 (155)
71 TOMMO_GENOMICS ss5149506041 Apr 25, 2021 (155)
72 EVA ss5237167742 Apr 25, 2021 (155)
73 1000G_HIGH_COVERAGE ss5246625068 Oct 12, 2022 (156)
74 HUGCELL_USP ss5446970950 Oct 12, 2022 (156)
75 EVA ss5506268976 Oct 12, 2022 (156)
76 1000G_HIGH_COVERAGE ss5521120377 Oct 12, 2022 (156)
77 EVA ss5624096266 Oct 12, 2022 (156)
78 SANFORD_IMAGENETICS ss5627927459 Oct 12, 2022 (156)
79 TOMMO_GENOMICS ss5677579052 Oct 12, 2022 (156)
80 YY_MCH ss5801855074 Oct 12, 2022 (156)
81 EVA ss5819543622 Oct 12, 2022 (156)
82 EVA ss5848506359 Oct 12, 2022 (156)
83 EVA ss5852352844 Oct 12, 2022 (156)
84 EVA ss5928696243 Oct 12, 2022 (156)
85 EVA ss5936514896 Oct 12, 2022 (156)
86 EVA ss5954111653 Oct 12, 2022 (156)
87 1000Genomes NC_000002.11 - 272840 Oct 11, 2018 (152)
88 1000Genomes_30x NC_000002.12 - 272840 Oct 12, 2022 (156)
89 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 272840 Oct 11, 2018 (152)
90 Genetic variation in the Estonian population NC_000002.11 - 272840 Oct 11, 2018 (152)
91 The Danish reference pan genome NC_000002.11 - 272840 Apr 25, 2020 (154)
92 gnomAD - Genomes NC_000002.12 - 272840 Apr 25, 2021 (155)
93 Genome of the Netherlands Release 5 NC_000002.11 - 272840 Apr 25, 2020 (154)
94 HapMap NC_000002.12 - 272840 Apr 25, 2020 (154)
95 KOREAN population from KRGDB NC_000002.11 - 272840 Apr 25, 2020 (154)
96 Northern Sweden NC_000002.11 - 272840 Jul 12, 2019 (153)
97 Qatari NC_000002.11 - 272840 Apr 25, 2020 (154)
98 SGDP_PRJ NC_000002.11 - 272840 Apr 25, 2020 (154)
99 Siberian NC_000002.11 - 272840 Apr 25, 2020 (154)
100 8.3KJPN NC_000002.11 - 272840 Apr 25, 2021 (155)
101 14KJPN NC_000002.12 - 272840 Oct 12, 2022 (156)
102 TopMed NC_000002.12 - 272840 Apr 25, 2021 (155)
103 UK 10K study - Twins NC_000002.11 - 272840 Oct 11, 2018 (152)
104 A Vietnamese Genetic Variation Database NC_000002.11 - 272840 Jul 12, 2019 (153)
105 ALFA NC_000002.12 - 272840 Apr 25, 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)
rs58123053 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85161941 NC_000002.9:262839:G:A NC_000002.12:272839:G:A (self)
ss91024107, ss109147744, ss117555793, ss162983273, ss163709400, ss199925355, ss210797466, ss276317459, ss284274179, ss292250660, ss1585800139, ss1712424571, ss3643209619 NC_000002.10:262839:G:A NC_000002.12:272839:G:A (self)
6472556, 3581212, 2532992, 4881882, 1574136, 3952663, 1362494, 1667756, 3424167, 895865, 7475348, 3581212, 781686, ss219014275, ss231001266, ss238594740, ss536810470, ss648873874, ss976398782, ss1068792278, ss1295582438, ss1428451286, ss1578701964, ss1602630786, ss1645624819, ss1919625826, ss1968672834, ss2020340171, ss2148379511, ss2624684676, ss2702931422, ss2768836856, ss2988844662, ss3344030882, ss3627972361, ss3638237703, ss3656794744, ss3728077629, ss3756248027, ss3783756057, ss3789358830, ss3794231480, ss3825593457, ss3826773108, ss3836791223, ss3851407187, ss3896775269, ss3984166889, ss3984166890, ss3986168732, ss4016975354, ss5149506041, ss5506268976, ss5624096266, ss5627927459, ss5819543622, ss5848506359, ss5936514896, ss5954111653 NC_000002.11:272839:G:A NC_000002.12:272839:G:A (self)
8646312, 46205478, 1718649, 11416156, 295345543, 4869154233, ss2226850179, ss3023933380, ss3646946600, ss3703087399, ss3800636576, ss3842204701, ss4491522664, ss5237167742, ss5246625068, ss5446970950, ss5521120377, ss5677579052, ss5801855074, ss5852352844, ss5928696243 NC_000002.12:272839:G:A NC_000002.12:272839:G:A (self)
ss65745944, ss74875785, ss96369845, ss106062968, ss119808197, ss135913181, ss138373948, ss156584402, ss172231186 NT_022221.13:262839:G:A NC_000002.12:272839:G:A (self)
ss21751386, ss23110780 NT_022327.13:262839:G:A NC_000002.12:272839:G:A (self)
3952663, ss3896775269 NC_000002.11:272839:G:C NC_000002.12:272839:G:C (self)
4869154233 NC_000002.12:272839:G:T NC_000002.12:272839:G:T (self)
Help

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

No publications for rs12714401

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