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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.

rs654916

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:55481535 (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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.004311 (1141/264690, TOPMED)
A=0.004041 (566/140050, GnomAD)
A=0.00000 (0/28258, 14KJPN) (+ 13 more)
A=0.00270 (50/18520, ALFA)
A=0.00000 (0/16756, 8.3KJPN)
A=0.0036 (23/6404, 1000G_30x)
A=0.0034 (17/5008, 1000G)
A=0.0000 (0/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.0003 (1/2930, KOREAN)
A=0.0000 (0/1832, Korea1K)
A=0.000 (0/600, NorthernSweden)
A=0.005 (3/558, SGDP_PRJ)
A=0.005 (1/216, Qatari)
A=0.00 (0/56, Siberian)
A=0.00 (0/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18520 A=0.00270 G=0.99730
European Sub 14152 A=0.00000 G=1.00000
African Sub 2898 A=0.0173 G=0.9827
African Others Sub 114 A=0.009 G=0.991
African American Sub 2784 A=0.0176 G=0.9824
Asian Sub 112 A=0.000 G=1.000
East Asian Sub 86 A=0.00 G=1.00
Other Asian Sub 26 A=0.00 G=1.00
Latin American 1 Sub 146 A=0.000 G=1.000
Latin American 2 Sub 610 A=0.000 G=1.000
South Asian Sub 98 A=0.00 G=1.00
Other Sub 504 A=0.000 G=1.000


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 A=0.004311 G=0.995689
gnomAD - Genomes Global Study-wide 140050 A=0.004041 G=0.995959
gnomAD - Genomes European Sub 75894 A=0.00005 G=0.99995
gnomAD - Genomes African Sub 41998 A=0.01276 G=0.98724
gnomAD - Genomes American Sub 13588 A=0.00088 G=0.99912
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.0000 G=1.0000
gnomAD - Genomes East Asian Sub 3096 A=0.0000 G=1.0000
gnomAD - Genomes Other Sub 2150 A=0.0065 G=0.9935
14KJPN JAPANESE Study-wide 28258 A=0.00000 G=1.00000
Allele Frequency Aggregator Total Global 18520 A=0.00270 G=0.99730
Allele Frequency Aggregator European Sub 14152 A=0.00000 G=1.00000
Allele Frequency Aggregator African Sub 2898 A=0.0173 G=0.9827
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.000 G=1.000
Allele Frequency Aggregator Other Sub 504 A=0.000 G=1.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.000 G=1.000
Allele Frequency Aggregator Asian Sub 112 A=0.000 G=1.000
Allele Frequency Aggregator South Asian Sub 98 A=0.00 G=1.00
8.3KJPN JAPANESE Study-wide 16756 A=0.00000 G=1.00000
1000Genomes_30x Global Study-wide 6404 A=0.0036 G=0.9964
1000Genomes_30x African Sub 1786 A=0.0129 G=0.9871
1000Genomes_30x Europe Sub 1266 A=0.0000 G=1.0000
1000Genomes_30x South Asian Sub 1202 A=0.0000 G=1.0000
1000Genomes_30x East Asian Sub 1170 A=0.0000 G=1.0000
1000Genomes_30x American Sub 980 A=0.000 G=1.000
1000Genomes Global Study-wide 5008 A=0.0034 G=0.9966
1000Genomes African Sub 1322 A=0.0129 G=0.9871
1000Genomes East Asian Sub 1008 A=0.0000 G=1.0000
1000Genomes Europe Sub 1006 A=0.0000 G=1.0000
1000Genomes South Asian Sub 978 A=0.000 G=1.000
1000Genomes American Sub 694 A=0.000 G=1.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.0000 G=1.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.0000 G=1.0000
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.0003 C=0.0000, G=0.9997, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.0000 G=1.0000
Northern Sweden ACPOP Study-wide 600 A=0.000 G=1.000
SGDP_PRJ Global Study-wide 558 A=0.005 G=0.995
Qatari Global Study-wide 216 A=0.005 G=0.995
Siberian Global Study-wide 56 A=0.00 G=1.00
The Danish reference pan genome Danish Study-wide 40 A=0.00 G=1.00
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 11 NC_000011.10:g.55481535A>C
GRCh38.p14 chr 11 NC_000011.10:g.55481535A>G
GRCh38.p14 chr 11 NC_000011.10:g.55481535A>T
GRCh37.p13 chr 11 NC_000011.9:g.55249011A>C
GRCh37.p13 chr 11 NC_000011.9:g.55249011A>G
GRCh37.p13 chr 11 NC_000011.9:g.55249011A>T
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 A= C G T
GRCh38.p14 chr 11 NC_000011.10:g.55481535= NC_000011.10:g.55481535A>C NC_000011.10:g.55481535A>G NC_000011.10:g.55481535A>T
GRCh37.p13 chr 11 NC_000011.9:g.55249011= NC_000011.9:g.55249011A>C NC_000011.9:g.55249011A>G NC_000011.9:g.55249011A>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#.

71 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss827950 Aug 11, 2000 (83)
2 WI_SSAHASNP ss12137607 Jul 11, 2003 (116)
3 SC_SNP ss15631380 Feb 27, 2004 (120)
4 SSAHASNP ss20759493 Apr 05, 2004 (121)
5 HGSV ss82323512 Dec 14, 2007 (130)
6 BCMHGSC_JDW ss88593633 Mar 24, 2008 (129)
7 HUMANGENOME_JCVI ss97387918 Feb 04, 2009 (130)
8 BGI ss106744476 Feb 04, 2009 (130)
9 ILLUMINA-UK ss119845257 Dec 01, 2009 (131)
10 ENSEMBL ss132554667 Dec 01, 2009 (131)
11 ENSEMBL ss137696908 Dec 01, 2009 (131)
12 GMI ss156334540 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss168401811 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss169949151 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss175141191 Jul 04, 2010 (132)
16 BUSHMAN ss202733592 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss207783070 Jul 04, 2010 (132)
18 1000GENOMES ss225251748 Jul 14, 2010 (132)
19 1000GENOMES ss235565768 Jul 15, 2010 (132)
20 1000GENOMES ss242197588 Jul 15, 2010 (132)
21 BL ss255178308 May 09, 2011 (134)
22 GMI ss281018416 May 04, 2012 (137)
23 GMI ss286384044 Apr 25, 2013 (138)
24 PJP ss291048882 May 09, 2011 (134)
25 TISHKOFF ss562570791 Apr 25, 2013 (138)
26 SSMP ss658077015 Apr 25, 2013 (138)
27 JMKIDD_LAB ss1077742306 Aug 21, 2014 (142)
28 1000GENOMES ss1341339094 Aug 21, 2014 (142)
29 DDI ss1426640232 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1575723473 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1626624715 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1669618748 Apr 01, 2015 (144)
33 HAMMER_LAB ss1806826368 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1931898530 Feb 12, 2016 (147)
35 GENOMED ss1967366650 Jul 19, 2016 (147)
36 JJLAB ss2026695224 Sep 14, 2016 (149)
37 USC_VALOUEV ss2154995867 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2627821590 Nov 08, 2017 (151)
39 GRF ss2699285434 Nov 08, 2017 (151)
40 GNOMAD ss2899835261 Nov 08, 2017 (151)
41 SWEGEN ss3008120316 Nov 08, 2017 (151)
42 CSHL ss3349608077 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3645197292 Oct 12, 2018 (152)
44 URBANLAB ss3649613591 Oct 12, 2018 (152)
45 EVA_DECODE ss3691817878 Jul 13, 2019 (153)
46 ACPOP ss3738193606 Jul 13, 2019 (153)
47 EVA ss3749316487 Jul 13, 2019 (153)
48 PACBIO ss3786958926 Jul 13, 2019 (153)
49 PACBIO ss3792100674 Jul 13, 2019 (153)
50 PACBIO ss3796982994 Jul 13, 2019 (153)
51 KHV_HUMAN_GENOMES ss3814663064 Jul 13, 2019 (153)
52 EVA ss3832636664 Apr 26, 2020 (154)
53 EVA ss3839874071 Apr 26, 2020 (154)
54 EVA ss3845353044 Apr 26, 2020 (154)
55 SGDP_PRJ ss3876292878 Apr 26, 2020 (154)
56 KRGDB ss3924642477 Apr 26, 2020 (154)
57 KOGIC ss3969931005 Apr 26, 2020 (154)
58 TOPMED ss4885814055 Apr 26, 2021 (155)
59 TOMMO_GENOMICS ss5202052514 Apr 26, 2021 (155)
60 1000G_HIGH_COVERAGE ss5287476260 Oct 13, 2022 (156)
61 EVA ss5399676771 Oct 13, 2022 (156)
62 HUGCELL_USP ss5482650141 Oct 13, 2022 (156)
63 1000G_HIGH_COVERAGE ss5583226051 Oct 13, 2022 (156)
64 SANFORD_IMAGENETICS ss5651256842 Oct 13, 2022 (156)
65 TOMMO_GENOMICS ss5749950116 Oct 13, 2022 (156)
66 YY_MCH ss5812429831 Oct 13, 2022 (156)
67 EVA ss5836682210 Oct 13, 2022 (156)
68 EVA ss5849986826 Oct 13, 2022 (156)
69 EVA ss5920041537 Oct 13, 2022 (156)
70 EVA ss5942567534 Oct 13, 2022 (156)
71 EVA ss5980677969 Oct 13, 2022 (156)
72 1000Genomes NC_000011.9 - 55249011 Oct 12, 2018 (152)
73 1000Genomes_30x NC_000011.10 - 55481535 Oct 13, 2022 (156)
74 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 55249011 Oct 12, 2018 (152)
75 The Danish reference pan genome NC_000011.9 - 55249011 Apr 26, 2020 (154)
76 gnomAD - Genomes NC_000011.10 - 55481535 Apr 26, 2021 (155)
77 KOREAN population from KRGDB NC_000011.9 - 55249011 Apr 26, 2020 (154)
78 Korean Genome Project NC_000011.10 - 55481535 Apr 26, 2020 (154)
79 Northern Sweden NC_000011.9 - 55249011 Jul 13, 2019 (153)
80 Qatari NC_000011.9 - 55249011 Apr 26, 2020 (154)
81 SGDP_PRJ NC_000011.9 - 55249011 Apr 26, 2020 (154)
82 Siberian NC_000011.9 - 55249011 Apr 26, 2020 (154)
83 8.3KJPN NC_000011.9 - 55249011 Apr 26, 2021 (155)
84 14KJPN NC_000011.10 - 55481535 Oct 13, 2022 (156)
85 TopMed NC_000011.10 - 55481535 Apr 26, 2021 (155)
86 UK 10K study - Twins NC_000011.9 - 55249011 Oct 12, 2018 (152)
87 ALFA NC_000011.10 - 55481535 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)
rs57172152 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
31819871, ss3924642477 NC_000011.9:55249010:A:C NC_000011.10:55481534:A:C (self)
ss82323512, ss88593633, ss119845257, ss168401811, ss169949151, ss175141191, ss202733592, ss207783070, ss255178308, ss281018416, ss286384044, ss291048882 NC_000011.8:55005586:A:G NC_000011.10:55481534:A:G (self)
53864002, 29912381, 2574040, 31819871, 11478471, 13940460, 28309858, 7512221, 60021821, 29912381, ss225251748, ss235565768, ss242197588, ss562570791, ss658077015, ss1077742306, ss1341339094, ss1426640232, ss1575723473, ss1626624715, ss1669618748, ss1806826368, ss1931898530, ss1967366650, ss2026695224, ss2154995867, ss2627821590, ss2699285434, ss2899835261, ss3008120316, ss3349608077, ss3738193606, ss3749316487, ss3786958926, ss3792100674, ss3796982994, ss3832636664, ss3839874071, ss3876292878, ss3924642477, ss5202052514, ss5399676771, ss5651256842, ss5836682210, ss5942567534, ss5980677969 NC_000011.9:55249010:A:G NC_000011.10:55481534:A:G (self)
70751986, 380195663, 26309006, 83787220, 101359711, 10106816159, ss3645197292, ss3649613591, ss3691817878, ss3814663064, ss3845353044, ss3969931005, ss4885814055, ss5287476260, ss5482650141, ss5583226051, ss5749950116, ss5812429831, ss5849986826, ss5920041537 NC_000011.10:55481534:A:G NC_000011.10:55481534:A:G (self)
ss12137607 NT_033903.5:348605:A:G NC_000011.10:55481534:A:G (self)
ss15631380, ss20759493 NT_033903.6:422052:A:G NC_000011.10:55481534:A:G (self)
ss827950, ss97387918, ss106744476, ss132554667, ss137696908, ss156334540 NT_167190.1:554805:A:G NC_000011.10:55481534:A:G (self)
31819871, ss3924642477 NC_000011.9:55249010:A:T NC_000011.10:55481534:A: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 rs654916

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.post761+d5e8e07