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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.

rs871626

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:20752492 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.11053 (6460/58444, ALFA)
C=0.07709 (2194/28459, GnomAD)
C=0.0238 (38/1599, 1000G_30x) (+ 8 more)
C=0.0251 (31/1233, 1000G)
C=0.103 (92/896, chrY)
C=0.007 (6/816, Daghestan)
C=0.084 (14/166, HapMap)
C=0.00 (0/52, Ancient Sardinia)
T=0.50 (12/24, GENOME_DK)
C=0.50 (12/24, GENOME_DK)
T=0.0 (0/4, SGDP_PRJ)
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 58444 T=0.88947 C=0.11053
European Sub 51882 T=0.88312 C=0.11688
African Sub 1346 T=0.9480 C=0.0520
African Others Sub 44 T=1.00 C=0.00
African American Sub 1302 T=0.9462 C=0.0538
Asian Sub 502 T=1.000 C=0.000
East Asian Sub 398 T=1.000 C=0.000
Other Asian Sub 104 T=1.000 C=0.000
Latin American 1 Sub 212 T=0.934 C=0.066
Latin American 2 Sub 1526 T=0.9738 C=0.0262
South Asian Sub 44 T=1.00 C=0.00
Other Sub 2932 T=0.9072 C=0.0928


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
Allele Frequency Aggregator Total Global 58444 T=0.88947 C=0.11053
Allele Frequency Aggregator European Sub 51882 T=0.88312 C=0.11688
Allele Frequency Aggregator Other Sub 2932 T=0.9072 C=0.0928
Allele Frequency Aggregator Latin American 2 Sub 1526 T=0.9738 C=0.0262
Allele Frequency Aggregator African Sub 1346 T=0.9480 C=0.0520
Allele Frequency Aggregator Asian Sub 502 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 212 T=0.934 C=0.066
Allele Frequency Aggregator South Asian Sub 44 T=1.00 C=0.00
gnomAD - Genomes Global Study-wide 28459 T=0.92291 C=0.07709
gnomAD - Genomes European Sub 15440 T=0.87863 C=0.12137
gnomAD - Genomes African Sub 7962 T=0.9724 C=0.0276
gnomAD - Genomes American Sub 3159 T=0.9769 C=0.0231
gnomAD - Genomes East Asian Sub 737 T=1.000 C=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 736 T=0.997 C=0.003
gnomAD - Genomes Other Sub 425 T=0.941 C=0.059
1000Genomes_30x Global Study-wide 1599 T=0.9762 C=0.0238
1000Genomes_30x African Sub 458 T=0.991 C=0.009
1000Genomes_30x South Asian Sub 319 T=1.000 C=0.000
1000Genomes_30x Europe Sub 305 T=0.902 C=0.098
1000Genomes_30x East Asian Sub 292 T=1.000 C=0.000
1000Genomes_30x American Sub 225 T=0.982 C=0.018
1000Genomes Global Study-wide 1233 T=0.9749 C=0.0251
1000Genomes African Sub 319 T=0.987 C=0.013
1000Genomes South Asian Sub 260 T=1.000 C=0.000
1000Genomes East Asian Sub 244 T=1.000 C=0.000
1000Genomes Europe Sub 240 T=0.896 C=0.104
1000Genomes American Sub 170 T=0.988 C=0.012
chrY_custom_capture Global Study-wide 896 T=0.897 C=0.103
chrY_custom_capture AFP Sub 0 T=0 C=0
chrY_custom_capture AHG Sub 0 T=0 C=0
chrY_custom_capture ASC Sub 0 T=0 C=0
chrY_custom_capture ASE Sub 0 T=0 C=0
chrY_custom_capture AUS Sub 0 T=0 C=0
chrY_custom_capture BRI Sub 0 T=0 C=0
chrY_custom_capture ENV Sub 0 T=0 C=0
chrY_custom_capture ESC Sub 0 T=0 C=0
chrY_custom_capture ESE Sub 0 T=0 C=0
chrY_custom_capture ESW Sub 0 T=0 C=0
chrY_custom_capture MEX Sub 0 T=0 C=0
chrY_custom_capture MNE Sub 0 T=0 C=0
chrY_custom_capture SCA Sub 0 T=0 C=0
Genome-wide autozygosity in Daghestan Global Study-wide 816 T=0.993 C=0.007
Genome-wide autozygosity in Daghestan Daghestan Sub 308 T=1.000 C=0.000
Genome-wide autozygosity in Daghestan Near_East Sub 144 T=1.000 C=0.000
Genome-wide autozygosity in Daghestan Central Asia Sub 122 T=1.000 C=0.000
Genome-wide autozygosity in Daghestan Europe Sub 108 T=0.944 C=0.056
Genome-wide autozygosity in Daghestan South Asian Sub 98 T=1.00 C=0.00
Genome-wide autozygosity in Daghestan Caucasus Sub 36 T=1.00 C=0.00
HapMap Global Study-wide 166 T=0.916 C=0.084
HapMap African Sub 60 T=1.00 C=0.00
HapMap American Sub 60 T=0.77 C=0.23
HapMap Asian Sub 46 T=1.00 C=0.00
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 52 T=1.00 C=0.00
The Danish reference pan genome Danish Study-wide 24 T=0.50 C=0.50
SGDP_PRJ Global Study-wide 4 T=0.0 C=1.0
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 Y NC_000024.10:g.20752492T>C
GRCh37.p13 chr Y NC_000024.9:g.22914378T>C
RPS4Y2 RefSeqGene NG_032924.1:g.1425T>C
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= C
GRCh38.p14 chr Y NC_000024.10:g.20752492= NC_000024.10:g.20752492T>C
GRCh37.p13 chr Y NC_000024.9:g.22914378= NC_000024.9:g.22914378T>C
RPS4Y2 RefSeqGene NG_032924.1:g.1425= NG_032924.1:g.1425T>C
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#.

62 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1294877 Oct 05, 2000 (86)
2 PERLEGEN ss24726441 Sep 20, 2004 (123)
3 ABI ss43985844 Mar 13, 2006 (126)
4 ILLUMINA ss75009035 Dec 06, 2007 (129)
5 AFFY ss76483974 Dec 06, 2007 (129)
6 KRIBB_YJKIM ss104829396 Feb 03, 2009 (130)
7 ILLUMINA ss160960286 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss162985030 Jul 04, 2010 (132)
9 ILLUMINA ss174757633 Jul 04, 2010 (132)
10 ILLUMINA ss481816638 May 04, 2012 (137)
11 ILLUMINA ss481849138 May 04, 2012 (137)
12 ILLUMINA ss482809664 Sep 08, 2015 (146)
13 ILLUMINA ss485702959 May 04, 2012 (137)
14 ILLUMINA ss537567877 Jul 19, 2016 (147)
15 ILLUMINA ss778630197 Sep 08, 2015 (146)
16 ILLUMINA ss783297053 Sep 08, 2015 (146)
17 ILLUMINA ss784249497 Sep 08, 2015 (146)
18 ILLUMINA ss832558367 Sep 08, 2015 (146)
19 ILLUMINA ss834087798 Sep 08, 2015 (146)
20 HAMMER_LAB ss1397805127 Sep 08, 2015 (146)
21 JOBLING_UOL ss1399965534 Apr 01, 2015 (144)
22 1000GENOMES ss1556782621 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1583557368 Apr 01, 2015 (144)
24 ILLUMINA ss1752815151 Sep 08, 2015 (146)
25 ILLUMINA ss1945970362 Feb 12, 2016 (147)
26 ILLUMINA ss1958181832 Feb 12, 2016 (147)
27 ILLUMINA ss1958181833 Feb 12, 2016 (147)
28 ILLUMINA ss2094839201 Dec 20, 2016 (150)
29 ILLUMINA ss2095230203 Dec 20, 2016 (150)
30 ILLUMINA ss2634994873 Nov 08, 2017 (151)
31 SWEGEN ss3020974909 Nov 08, 2017 (151)
32 ILLUMINA ss3023055323 Nov 08, 2017 (151)
33 ILLUMINA ss3023055324 Nov 08, 2017 (151)
34 HUMGEN ss3029951978 Nov 08, 2017 (151)
35 ILLUMINA ss3626006179 Oct 12, 2018 (152)
36 ILLUMINA ss3630505256 Oct 12, 2018 (152)
37 ILLUMINA ss3632877766 Oct 12, 2018 (152)
38 ILLUMINA ss3633571208 Oct 12, 2018 (152)
39 ILLUMINA ss3634301568 Oct 12, 2018 (152)
40 ILLUMINA ss3635265398 Oct 12, 2018 (152)
41 ILLUMINA ss3635978348 Oct 12, 2018 (152)
42 ILLUMINA ss3637015619 Oct 12, 2018 (152)
43 ILLUMINA ss3637732105 Oct 12, 2018 (152)
44 ILLUMINA ss3638887532 Oct 12, 2018 (152)
45 ILLUMINA ss3640972888 Oct 12, 2018 (152)
46 ILLUMINA ss3641266713 Oct 12, 2018 (152)
47 ILLUMINA ss3641565726 Oct 12, 2018 (152)
48 ILLUMINA ss3643810250 Oct 12, 2018 (152)
49 ILLUMINA ss3645022159 Oct 12, 2018 (152)
50 ILLUMINA ss3653613968 Oct 12, 2018 (152)
51 ILLUMINA ss3653613969 Oct 12, 2018 (152)
52 ILLUMINA ss3726714821 Jul 14, 2019 (153)
53 ILLUMINA ss3744336952 Jul 14, 2019 (153)
54 ILLUMINA ss3745565396 Jul 14, 2019 (153)
55 ILLUMINA ss3773057001 Jul 14, 2019 (153)
56 SGDP_PRJ ss3892775832 Apr 27, 2020 (154)
57 EVA ss3986004813 Apr 27, 2021 (155)
58 GNOMAD ss4126295879 Apr 27, 2021 (155)
59 1000G_HIGH_COVERAGE ss5623875507 Oct 13, 2022 (156)
60 SANFORD_IMAGENETICS ss5666150205 Oct 13, 2022 (156)
61 EVA ss5848242907 Oct 13, 2022 (156)
62 EVA ss5979925771 Oct 13, 2022 (156)
63 1000Genomes NC_000024.9 - 22914378 Oct 12, 2018 (152)
64 1000Genomes_30x NC_000024.10 - 20752492 Oct 13, 2022 (156)
65 chrY_custom_capture NC_000024.9 - 22914378 Apr 27, 2020 (154)
66 Genome-wide autozygosity in Daghestan NC_000024.8 - 21323766 Apr 27, 2020 (154)
67 The Danish reference pan genome NC_000024.9 - 22914378 Apr 27, 2020 (154)
68 gnomAD - Genomes NC_000024.10 - 20752492 Apr 27, 2021 (155)
69 HapMap NC_000024.10 - 20752492 Apr 27, 2020 (154)
70 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 22914378 Apr 27, 2021 (155)
71 SGDP_PRJ NC_000024.9 - 22914378 Apr 27, 2020 (154)
72 ALFA NC_000024.10 - 20752492 Apr 27, 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)
rs17250394 Oct 07, 2004 (123)
rs386618267 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
556056, ss76483974, ss162985030, ss481816638, ss1397805127, ss3643810250 NC_000024.8:21323765:T:C NC_000024.10:20752491:T:C (self)
84735609, 12797, 9722305, 1230740, 44792812, ss481849138, ss482809664, ss485702959, ss537567877, ss778630197, ss783297053, ss784249497, ss832558367, ss834087798, ss1399965534, ss1556782621, ss1583557368, ss1752815151, ss1945970362, ss1958181832, ss1958181833, ss2094839201, ss2095230203, ss2634994873, ss3020974909, ss3023055323, ss3023055324, ss3029951978, ss3626006179, ss3630505256, ss3632877766, ss3633571208, ss3634301568, ss3635265398, ss3635978348, ss3637015619, ss3637732105, ss3638887532, ss3640972888, ss3641266713, ss3641565726, ss3645022159, ss3653613968, ss3653613969, ss3744336952, ss3745565396, ss3773057001, ss3892775832, ss3986004813, ss5666150205, ss5848242907, ss5979925771 NC_000024.9:22914377:T:C NC_000024.10:20752491:T:C (self)
111401442, 595130273, 4060813, 14097096778, ss3726714821, ss4126295879, ss5623875507 NC_000024.10:20752491:T:C NC_000024.10:20752491:T:C (self)
ss1294877, ss24726441, ss43985844, ss75009035, ss104829396, ss160960286, ss174757633 NT_011875.12:9115799:T:C NC_000024.10:20752491: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.

No publications for rs871626

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