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dbSNP Short Genetic Variations

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.

rs200661132

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:15985369 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00020 (6/29951, GnomAD)
G=0.0004 (1/2642, ALFA)
G=0.0125 (20/1599, 1000G_30x) (+ 3 more)
G=0.0100 (14/1400, KOREAN)
G=0.00 (0/14, Ancient Sardinia)
A=0.0 (0/2, 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 2642 A=0.9996 G=0.0004
European Sub 2514 A=0.9996 G=0.0004
African Sub 24 A=1.00 G=0.00
African Others Sub 0 A=0 G=0
African American Sub 24 A=1.00 G=0.00
Asian Sub 4 A=1.0 G=0.0
East Asian Sub 4 A=1.0 G=0.0
Other Asian Sub 0 A=0 G=0
Latin American 1 Sub 2 A=1.0 G=0.0
Latin American 2 Sub 28 A=1.00 G=0.00
South Asian Sub 4 A=1.0 G=0.0
Other Sub 66 A=1.00 G=0.00


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
gnomAD - Genomes Global Study-wide 29951 A=0.99980 G=0.00020
gnomAD - Genomes European Sub 16398 A=1.00000 G=0.00000
gnomAD - Genomes African Sub 8341 A=1.0000 G=0.0000
gnomAD - Genomes American Sub 3240 A=0.9994 G=0.0006
gnomAD - Genomes East Asian Sub 760 A=0.995 G=0.005
gnomAD - Genomes Ashkenazi Jewish Sub 753 A=1.000 G=0.000
gnomAD - Genomes Other Sub 459 A=1.000 G=0.000
Allele Frequency Aggregator Total Global 2642 A=0.9996 G=0.0004
Allele Frequency Aggregator European Sub 2514 A=0.9996 G=0.0004
Allele Frequency Aggregator Other Sub 66 A=1.00 G=0.00
Allele Frequency Aggregator Latin American 2 Sub 28 A=1.00 G=0.00
Allele Frequency Aggregator African Sub 24 A=1.00 G=0.00
Allele Frequency Aggregator South Asian Sub 4 A=1.0 G=0.0
Allele Frequency Aggregator Asian Sub 4 A=1.0 G=0.0
Allele Frequency Aggregator Latin American 1 Sub 2 A=1.0 G=0.0
1000Genomes_30x Global Study-wide 1599 A=0.9875 G=0.0125
1000Genomes_30x African Sub 458 A=1.000 G=0.000
1000Genomes_30x South Asian Sub 319 A=1.000 G=0.000
1000Genomes_30x Europe Sub 305 A=1.000 G=0.000
1000Genomes_30x East Asian Sub 292 A=0.932 G=0.068
1000Genomes_30x American Sub 225 A=1.000 G=0.000
KOREAN population from KRGDB KOREAN Study-wide 1400 A=0.9900 G=0.0100
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 14 A=1.00 G=0.00
SGDP_PRJ Global Study-wide 2 A=0.0 G=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.15985369A>G
GRCh37.p13 chr Y NC_000024.9:g.18097249A>G
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= G
GRCh38.p14 chr Y NC_000024.10:g.15985369= NC_000024.10:g.15985369A>G
GRCh37.p13 chr Y NC_000024.9:g.18097249= NC_000024.9:g.18097249A>G
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#.

21 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss283923205 May 04, 2012 (137)
2 ILLUMINA ss532727939 Jul 19, 2016 (147)
3 ILLUMINA ss780636014 Sep 08, 2015 (146)
4 ILLUMINA ss783353342 Sep 08, 2015 (146)
5 ILLUMINA ss836130063 Sep 08, 2015 (146)
6 ILLUMINA ss1945969451 Feb 12, 2016 (147)
7 ILLUMINA ss1958178529 Feb 12, 2016 (147)
8 HUMAN_LONGEVITY ss2321445429 Dec 20, 2016 (150)
9 ILLUMINA ss2634994380 Nov 08, 2017 (151)
10 ILLUMINA ss3023054231 Nov 08, 2017 (151)
11 ILLUMINA ss3630504751 Oct 12, 2018 (152)
12 ILLUMINA ss3632877273 Oct 12, 2018 (152)
13 ILLUMINA ss3653612801 Oct 12, 2018 (152)
14 ILLUMINA ss3744336552 Jul 14, 2019 (153)
15 SGDP_PRJ ss3892730728 Apr 27, 2020 (154)
16 KRGDB ss3943522132 Apr 27, 2020 (154)
17 EVA ss3984772642 Apr 27, 2021 (155)
18 EVA ss3985996130 Apr 27, 2021 (155)
19 GNOMAD ss4126201888 Apr 27, 2021 (155)
20 1000G_HIGH_COVERAGE ss5623843008 Oct 13, 2022 (156)
21 SANFORD_IMAGENETICS ss5666141291 Oct 13, 2022 (156)
22 1000Genomes_30x NC_000024.10 - 15985369 Oct 13, 2022 (156)
23 gnomAD - Genomes NC_000024.10 - 15985369 Apr 27, 2021 (155)
24 KOREAN population from KRGDB NC_000024.9 - 18097249 Apr 27, 2020 (154)
25 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 18097249 Apr 27, 2021 (155)
26 SGDP_PRJ NC_000024.9 - 18097249 Apr 27, 2020 (154)
27 ALFA NC_000024.10 - 15985369 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)
rs386419966 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss283923205 NC_000024.8:16606642:A:G NC_000024.10:15985368:A:G (self)
50699526, 1222057, 44747708, ss532727939, ss780636014, ss783353342, ss836130063, ss1945969451, ss1958178529, ss2634994380, ss3023054231, ss3630504751, ss3632877273, ss3653612801, ss3744336552, ss3892730728, ss3943522132, ss3984772642, ss3985996130, ss5666141291 NC_000024.9:18097248:A:G NC_000024.10:15985368:A:G (self)
111368943, 595035833, 7260968532, ss2321445429, ss4126201888, ss5623843008 NC_000024.10:15985368:A:G NC_000024.10:15985368:A:G (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 rs200661132

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