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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.

rs2740980

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:12312201 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.03396 (1319/38836, ALFA)
A=0.02434 (736/30237, GnomAD)
A=0.0175 (28/1599, 1000G_30x) (+ 1 more)
C=0.0000 (0/1410, KOREAN)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 38836 G=0.96604 A=0.03396
European Sub 35648 G=0.96460 A=0.03540
African Sub 534 G=0.989 A=0.011
African Others Sub 24 G=1.00 A=0.00
African American Sub 510 G=0.988 A=0.012
Asian Sub 1576 G=1.0000 A=0.0000
East Asian Sub 1280 G=1.0000 A=0.0000
Other Asian Sub 296 G=1.000 A=0.000
Latin American 1 Sub 142 G=0.915 A=0.085
Latin American 2 Sub 150 G=0.907 A=0.093
South Asian Sub 120 G=0.983 A=0.017
Other Sub 666 G=0.965 A=0.035


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 38836 G=0.96604 A=0.03396
Allele Frequency Aggregator European Sub 35648 G=0.96460 A=0.03540
Allele Frequency Aggregator Asian Sub 1576 G=1.0000 A=0.0000
Allele Frequency Aggregator Other Sub 666 G=0.965 A=0.035
Allele Frequency Aggregator African Sub 534 G=0.989 A=0.011
Allele Frequency Aggregator Latin American 2 Sub 150 G=0.907 A=0.093
Allele Frequency Aggregator Latin American 1 Sub 142 G=0.915 A=0.085
Allele Frequency Aggregator South Asian Sub 120 G=0.983 A=0.017
gnomAD - Genomes Global Study-wide 30237 G=0.97566 A=0.02434
gnomAD - Genomes European Sub 16413 G=0.97295 A=0.02705
gnomAD - Genomes African Sub 8537 G=0.9947 A=0.0053
gnomAD - Genomes American Sub 3290 G=0.9477 A=0.0523
gnomAD - Genomes East Asian Sub 770 G=1.000 A=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 754 G=0.920 A=0.080
gnomAD - Genomes Other Sub 473 G=0.968 A=0.032
1000Genomes_30x Global Study-wide 1599 G=0.9825 A=0.0175
1000Genomes_30x African Sub 458 G=0.996 A=0.004
1000Genomes_30x South Asian Sub 319 G=0.966 A=0.034
1000Genomes_30x Europe Sub 305 G=0.970 A=0.030
1000Genomes_30x East Asian Sub 292 G=0.997 A=0.003
1000Genomes_30x American Sub 225 G=0.978 A=0.022
KOREAN population from KRGDB KOREAN Study-wide 1410 G=0.0007 C=0.0000
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.12312201G>A
GRCh38.p14 chr Y NC_000024.10:g.12312201G>C
GRCh37.p13 chr Y NC_000024.9:g.14432928A>G
GRCh37.p13 chr Y NC_000024.9:g.14432928A>C
LOC106128902 genomic region NG_042306.1:g.107G>A
LOC106128902 genomic region NG_042306.1:g.107G>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 G= A C
GRCh38.p14 chr Y NC_000024.10:g.12312201= NC_000024.10:g.12312201G>A NC_000024.10:g.12312201G>C
GRCh37.p13 chr Y NC_000024.9:g.14432928A>G NC_000024.9:g.14432928= NC_000024.9:g.14432928A>C
LOC106128902 genomic region NG_042306.1:g.107= NG_042306.1:g.107G>A NG_042306.1:g.107G>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#.

59 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3868810 Sep 28, 2001 (100)
2 BCM_SSAHASNP ss10581023 Jul 11, 2003 (123)
3 WI_SSAHASNP ss14424400 Dec 05, 2003 (119)
4 SSAHASNP ss22884533 Apr 05, 2004 (121)
5 ABI ss43757992 Mar 14, 2006 (126)
6 BCMHGSC_JDW ss94449854 Mar 25, 2008 (129)
7 BGI ss105778221 Feb 05, 2009 (130)
8 ILLUMINA-UK ss115581737 Feb 05, 2009 (130)
9 ENSEMBL ss133780833 Dec 01, 2009 (131)
10 ENSEMBL ss144449139 Dec 01, 2009 (131)
11 GMI ss157857760 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss162981940 Jul 04, 2010 (132)
13 COMPLETE_GENOMICS ss166082323 Jul 04, 2010 (132)
14 BUSHMAN ss204417435 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss208951130 Jul 04, 2010 (132)
16 BL ss255899713 May 09, 2011 (134)
17 GMI ss283921868 May 04, 2012 (137)
18 GMI ss287665958 Apr 25, 2013 (138)
19 PJP ss294561837 May 09, 2011 (134)
20 ILLUMINA ss537122470 Jul 19, 2016 (147)
21 TISHKOFF ss567113898 Apr 25, 2013 (138)
22 SSMP ss663096329 Apr 25, 2013 (138)
23 ILLUMINA ss778701541 Sep 08, 2015 (146)
24 ILLUMINA ss834160511 Sep 08, 2015 (146)
25 DDI ss1432160118 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1583555519 Apr 01, 2015 (144)
27 ILLUMINA ss1945968623 Feb 12, 2016 (147)
28 ILLUMINA ss1958175915 Feb 12, 2016 (147)
29 ILLUMINA ss1958175916 Feb 12, 2016 (147)
30 USC_VALOUEV ss2159352205 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2321402908 Dec 20, 2016 (150)
32 SYSTEMSBIOZJU ss2629804530 Nov 08, 2017 (151)
33 ILLUMINA ss2634993853 Nov 08, 2017 (151)
34 GRF ss2710438262 Nov 08, 2017 (151)
35 SWEGEN ss3020945222 Nov 08, 2017 (151)
36 ILLUMINA ss3023052920 Nov 08, 2017 (151)
37 ILLUMINA ss3023052921 Nov 08, 2017 (151)
38 ILLUMINA ss3626005291 Oct 12, 2018 (152)
39 ILLUMINA ss3630504201 Oct 12, 2018 (152)
40 ILLUMINA ss3632876762 Oct 12, 2018 (152)
41 ILLUMINA ss3641265848 Oct 12, 2018 (152)
42 ILLUMINA ss3641564752 Oct 12, 2018 (152)
43 ILLUMINA ss3645021245 Oct 12, 2018 (152)
44 ILLUMINA ss3653611388 Oct 12, 2018 (152)
45 ILLUMINA ss3653611389 Oct 12, 2018 (152)
46 ILLUMINA ss3726713110 Jul 14, 2019 (153)
47 ILLUMINA ss3744336107 Jul 14, 2019 (153)
48 PACBIO ss3788975628 Jul 14, 2019 (153)
49 PACBIO ss3793845987 Jul 14, 2019 (153)
50 PACBIO ss3798730479 Jul 14, 2019 (153)
51 EVA ss3836373057 Apr 27, 2020 (154)
52 SGDP_PRJ ss3892700276 Apr 27, 2020 (154)
53 KRGDB ss3943498621 Apr 27, 2020 (154)
54 EVA ss3984771871 Apr 27, 2021 (155)
55 EVA ss3985986959 Apr 27, 2021 (155)
56 GNOMAD ss4126115751 Apr 27, 2021 (155)
57 ESTONIANBIOCENTRE ss5237680863 Oct 17, 2022 (156)
58 1000G_HIGH_COVERAGE ss5623814469 Oct 17, 2022 (156)
59 SANFORD_IMAGENETICS ss5666135836 Oct 17, 2022 (156)
60 1000Genomes_30x NC_000024.10 - 12312201 Oct 17, 2022 (156)
61 gnomAD - Genomes NC_000024.10 - 12312201 Apr 27, 2021 (155)
62 KOREAN population from KRGDB NC_000024.9 - 14432928 Apr 27, 2020 (154)
63 ALFA NC_000024.10 - 12312201 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)
rs7067472 Oct 07, 2004 (123)
rs35308108 May 23, 2006 (127)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss94449854, ss162981940, ss166082323, ss204417435, ss208951130, ss255899713, ss283921868, ss287665958, ss294561837 NC_000024.8:12942935:A:A NC_000024.10:12312200:G:A (self)
50676015, ss537122470, ss567113898, ss663096329, ss778701541, ss834160511, ss1432160118, ss1583555519, ss1945968623, ss1958175915, ss1958175916, ss2159352205, ss2629804530, ss2634993853, ss2710438262, ss3020945222, ss3023052920, ss3023052921, ss3626005291, ss3630504201, ss3632876762, ss3641265848, ss3641564752, ss3645021245, ss3653611388, ss3653611389, ss3744336107, ss3788975628, ss3793845987, ss3798730479, ss3836373057, ss3892700276, ss3943498621, ss3984771871, ss3985986959, ss5237680863, ss5666135836 NC_000024.9:14432927:A:A NC_000024.10:12312200:G:A (self)
111340404, 594949586, 8673653758, ss2321402908, ss3726713110, ss4126115751, ss5623814469 NC_000024.10:12312200:G:A NC_000024.10:12312200:G:A (self)
ss10581023 NT_011875.9:634357:A:A NC_000024.10:12312200:G:A (self)
ss3868810, ss14424400, ss22884533, ss43757992, ss105778221, ss115581737, ss133780833, ss144449139, ss157857760 NT_011875.12:634349:A:A NC_000024.10:12312200:G:A (self)
50676015, ss3943498621 NC_000024.9:14432927:A:C NC_000024.10:12312200:G: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 rs2740980
PMID Title Author Year Journal
19495413 Improved resolution haplogroup G phylogeny in the Y chromosome, revealed by a set of newly characterized SNPs. Sims LM et al. 2009 PloS one
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