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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.

rs1462146

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:106538455 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.065053 (17219/264690, TOPMED)
A=0.061743 (8651/140112, GnomAD)
A=0.013841 (1809/130698, ALFA) (+ 10 more)
A=0.0678 (434/6404, 1000G_30x)
A=0.0645 (323/5008, 1000G)
A=0.0003 (1/3854, ALSPAC)
A=0.0008 (3/3708, TWINSUK)
A=0.0216 (45/2084, HGDP_Stanford)
A=0.1797 (197/1096, HapMap)
A=0.002 (2/998, GoNL)
A=0.019 (4/216, Qatari)
A=0.00 (0/98, Ancient Sardinia)
G=0.45 (10/22, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CRYBG1 : Intron 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 130698 G=0.986159 A=0.013841 0.97446 0.002142 0.023397 32
European Sub 110814 G=0.997825 A=0.002175 0.995686 0.000036 0.004277 7
African Sub 6610 G=0.7980 A=0.2020 0.635401 0.039334 0.325265 0
African Others Sub 238 G=0.794 A=0.206 0.647059 0.058824 0.294118 1
African American Sub 6372 G=0.7982 A=0.2018 0.634965 0.038606 0.326428 0
Asian Sub 620 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 488 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 132 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 1 Sub 734 G=0.939 A=0.061 0.880109 0.002725 0.117166 0
Latin American 2 Sub 6260 G=0.9877 A=0.0123 0.975719 0.000319 0.023962 0
South Asian Sub 184 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Sub 5476 G=0.9797 A=0.0203 0.961651 0.002191 0.036158 12


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=0.934947 A=0.065053
gnomAD - Genomes Global Study-wide 140112 G=0.938257 A=0.061743
gnomAD - Genomes European Sub 75928 G=0.99879 A=0.00121
gnomAD - Genomes African Sub 41938 G=0.80664 A=0.19336
gnomAD - Genomes American Sub 13644 G=0.97515 A=0.02485
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9937 A=0.0063
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9581 A=0.0419
Allele Frequency Aggregator Total Global 130698 G=0.986159 A=0.013841
Allele Frequency Aggregator European Sub 110814 G=0.997825 A=0.002175
Allele Frequency Aggregator African Sub 6610 G=0.7980 A=0.2020
Allele Frequency Aggregator Latin American 2 Sub 6260 G=0.9877 A=0.0123
Allele Frequency Aggregator Other Sub 5476 G=0.9797 A=0.0203
Allele Frequency Aggregator Latin American 1 Sub 734 G=0.939 A=0.061
Allele Frequency Aggregator Asian Sub 620 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 184 G=1.000 A=0.000
1000Genomes_30x Global Study-wide 6404 G=0.9322 A=0.0678
1000Genomes_30x African Sub 1786 G=0.7704 A=0.2296
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.976 A=0.024
1000Genomes Global Study-wide 5008 G=0.9355 A=0.0645
1000Genomes African Sub 1322 G=0.7685 A=0.2315
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.976 A=0.024
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9997 A=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9992 A=0.0008
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.9784 A=0.0216
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=1.000 A=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.998 A=0.002
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.974 A=0.026
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=1.000 A=0.000
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.855 A=0.145
HGDP-CEPH-db Supplement 1 America Sub 216 G=1.000 A=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=1.00 A=0.00
HapMap Global Study-wide 1096 G=0.8203 A=0.1797
HapMap African Sub 692 G=0.762 A=0.238
HapMap American Sub 318 G=0.899 A=0.101
HapMap Asian Sub 86 G=1.00 A=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.998 A=0.002
Qatari Global Study-wide 216 G=0.981 A=0.019
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 98 G=1.00 A=0.00
SGDP_PRJ Global Study-wide 22 G=0.45 A=0.55
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 6 NC_000006.12:g.106538455G>A
GRCh37.p13 chr 6 NC_000006.11:g.106986330G>A
Gene: CRYBG1, crystallin beta-gamma domain containing 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CRYBG1 transcript variant 1 NM_001371242.2:c.4719-948…

NM_001371242.2:c.4719-948G>A

 		N/A Intron Variant
CRYBG1 transcript variant 2 NM_001624.4:c.3495-948G>A N/A Intron Variant
CRYBG1 transcript variant X1 XM_047418270.1:c.4797-948…

XM_047418270.1:c.4797-948G>A

 		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
GRCh38.p14 chr 6 NC_000006.12:g.106538455= NC_000006.12:g.106538455G>A
GRCh37.p13 chr 6 NC_000006.11:g.106986330= NC_000006.11:g.106986330G>A
CRYBG1 transcript variant 1 NM_001371242.2:c.4719-948= NM_001371242.2:c.4719-948G>A
AIM1 transcript NM_001624.2:c.3495-948= NM_001624.2:c.3495-948G>A
CRYBG1 transcript variant 2 NM_001624.4:c.3495-948= NM_001624.4:c.3495-948G>A
AIM1 transcript variant X1 XM_005266839.1:c.4719-948= XM_005266839.1:c.4719-948G>A
CRYBG1 transcript variant X1 XM_047418270.1:c.4797-948= XM_047418270.1:c.4797-948G>A
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#.

63 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2281840 Oct 23, 2000 (88)
2 SC_JCM ss3953731 Sep 28, 2001 (100)
3 WI_SSAHASNP ss11800069 Jul 11, 2003 (116)
4 ILLUMINA ss67446799 Dec 01, 2006 (127)
5 ILLUMINA ss71169586 May 17, 2007 (127)
6 ILLUMINA ss75417129 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss119393798 Dec 01, 2009 (131)
8 ILLUMINA ss160357090 Dec 01, 2009 (131)
9 ILLUMINA ss172519950 Jul 04, 2010 (132)
10 1000GENOMES ss222594413 Jul 14, 2010 (132)
11 ILLUMINA ss479985911 May 04, 2012 (137)
12 ILLUMINA ss479994674 May 04, 2012 (137)
13 ILLUMINA ss480646126 Sep 08, 2015 (146)
14 ILLUMINA ss484791136 May 04, 2012 (137)
15 ILLUMINA ss536875783 Sep 08, 2015 (146)
16 TISHKOFF ss559431482 Apr 25, 2013 (138)
17 ILLUMINA ss778433544 Sep 08, 2015 (146)
18 ILLUMINA ss782842230 Aug 21, 2014 (142)
19 ILLUMINA ss783806895 Sep 08, 2015 (146)
20 ILLUMINA ss832095972 Apr 01, 2015 (144)
21 ILLUMINA ss833889024 Sep 08, 2015 (146)
22 EVA-GONL ss983340235 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1073913522 Aug 21, 2014 (142)
24 1000GENOMES ss1321663254 Aug 21, 2014 (142)
25 DDI ss1430851065 Apr 01, 2015 (144)
26 EVA_DECODE ss1592900702 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1616370858 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1659364891 Apr 01, 2015 (144)
29 ILLUMINA ss1752593949 Sep 08, 2015 (146)
30 HAMMER_LAB ss1804604506 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1926588286 Feb 12, 2016 (147)
32 HUMAN_LONGEVITY ss2287088677 Dec 20, 2016 (150)
33 ILLUMINA ss2634493407 Nov 08, 2017 (151)
34 GNOMAD ss2843355438 Nov 08, 2017 (151)
35 SWEGEN ss2999705214 Nov 08, 2017 (151)
36 ILLUMINA ss3629622954 Oct 12, 2018 (152)
37 ILLUMINA ss3632407792 Oct 12, 2018 (152)
38 ILLUMINA ss3633432830 Oct 12, 2018 (152)
39 ILLUMINA ss3634156222 Oct 12, 2018 (152)
40 ILLUMINA ss3635081866 Oct 12, 2018 (152)
41 ILLUMINA ss3635836785 Oct 12, 2018 (152)
42 ILLUMINA ss3636806568 Oct 12, 2018 (152)
43 ILLUMINA ss3637589632 Oct 12, 2018 (152)
44 ILLUMINA ss3638648951 Oct 12, 2018 (152)
45 ILLUMINA ss3640789167 Oct 12, 2018 (152)
46 ILLUMINA ss3643588639 Oct 12, 2018 (152)
47 ILLUMINA ss3745381803 Jul 13, 2019 (153)
48 ILLUMINA ss3772875244 Jul 13, 2019 (153)
49 KHV_HUMAN_GENOMES ss3808638226 Jul 13, 2019 (153)
50 HGDP ss3847845702 Apr 26, 2020 (154)
51 SGDP_PRJ ss3865388575 Apr 26, 2020 (154)
52 EVA ss3985242948 Apr 26, 2021 (155)
53 EVA ss4017292179 Apr 26, 2021 (155)
54 TOPMED ss4716469264 Apr 26, 2021 (155)
55 1000G_HIGH_COVERAGE ss5269809761 Oct 13, 2022 (156)
56 EVA ss5368034060 Oct 13, 2022 (156)
57 HUGCELL_USP ss5467303854 Oct 13, 2022 (156)
58 EVA ss5508651644 Oct 13, 2022 (156)
59 1000G_HIGH_COVERAGE ss5556474517 Oct 13, 2022 (156)
60 SANFORD_IMAGENETICS ss5641184240 Oct 13, 2022 (156)
61 EVA ss5842780288 Oct 13, 2022 (156)
62 EVA ss5885338684 Oct 13, 2022 (156)
63 EVA ss5969699488 Oct 13, 2022 (156)
64 1000Genomes NC_000006.11 - 106986330 Oct 12, 2018 (152)
65 1000Genomes_30x NC_000006.12 - 106538455 Oct 13, 2022 (156)
66 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 106986330 Oct 12, 2018 (152)
67 gnomAD - Genomes NC_000006.12 - 106538455 Apr 26, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000006.11 - 106986330 Apr 26, 2020 (154)
69 HGDP-CEPH-db Supplement 1 NC_000006.10 - 107093023 Apr 26, 2020 (154)
70 HapMap NC_000006.12 - 106538455 Apr 26, 2020 (154)
71 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000006.11 - 106986330 Apr 26, 2021 (155)
72 Qatari NC_000006.11 - 106986330 Apr 26, 2020 (154)
73 SGDP_PRJ NC_000006.11 - 106986330 Apr 26, 2020 (154)
74 TopMed NC_000006.12 - 106538455 Apr 26, 2021 (155)
75 UK 10K study - Twins NC_000006.11 - 106986330 Oct 12, 2018 (152)
76 ALFA NC_000006.12 - 106538455 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
523594, ss479985911, ss1592900702, ss3643588639, ss3847845702 NC_000006.10:107093022:G:A NC_000006.12:106538454:G:A (self)
33508784, 18669395, 8318832, 468875, 8630216, 17405555, 18669395, ss222594413, ss479994674, ss480646126, ss484791136, ss536875783, ss559431482, ss778433544, ss782842230, ss783806895, ss832095972, ss833889024, ss983340235, ss1073913522, ss1321663254, ss1430851065, ss1616370858, ss1659364891, ss1752593949, ss1804604506, ss1926588286, ss2634493407, ss2843355438, ss2999705214, ss3629622954, ss3632407792, ss3633432830, ss3634156222, ss3635081866, ss3635836785, ss3636806568, ss3637589632, ss3638648951, ss3640789167, ss3745381803, ss3772875244, ss3865388575, ss3985242948, ss4017292179, ss5368034060, ss5508651644, ss5641184240, ss5842780288, ss5969699488 NC_000006.11:106986329:G:A NC_000006.12:106538454:G:A (self)
44000452, 236581908, 3215081, 553846822, 13963392865, ss2287088677, ss3808638226, ss4716469264, ss5269809761, ss5467303854, ss5556474517, ss5885338684 NC_000006.12:106538454:G:A NC_000006.12:106538454:G:A (self)
ss11800069 NT_025741.12:11155758:G:A NC_000006.12:106538454:G:A (self)
ss2281840, ss3953731, ss67446799, ss71169586, ss75417129, ss119393798, ss160357090, ss172519950 NT_025741.15:11155786:G:A NC_000006.12:106538454:G:A (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 rs1462146
PMID Title Author Year Journal
21668797 A genome-wide association study of DSM-IV cannabis dependence. Agrawal A et al. 2011 Addiction biology
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