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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.

rs16980621

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:11939602 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.20510 (5996/29234, GnomAD)
C=0.06772 (1905/28130, ALFA)
C=0.2639 (422/1599, 1000G_30x) (+ 8 more)
C=0.2409 (297/1233, 1000G)
C=0.092 (82/896, chrY)
C=0.064 (52/816, Daghestan)
C=0.11 (6/53, Qatari)
A=0.00 (0/46, SGDP_PRJ)
C=0.00 (0/22, Ancient Sardinia)
C=0.10 (2/20, GENOME_DK)
A=0.0 (0/2, Siberian)
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 28130 A=0.93228 C=0.06772
European Sub 26024 A=0.94655 C=0.05345
African Sub 714 A=0.454 C=0.546
African Others Sub 24 A=0.08 C=0.92
African American Sub 690 A=0.467 C=0.533
Asian Sub 564 A=0.996 C=0.004
East Asian Sub 492 A=0.996 C=0.004
Other Asian Sub 72 A=1.00 C=0.00
Latin American 1 Sub 122 A=0.672 C=0.328
Latin American 2 Sub 140 A=0.943 C=0.057
South Asian Sub 112 A=1.000 C=0.000
Other Sub 454 A=0.837 C=0.163


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 29234 A=0.79490 C=0.20510
gnomAD - Genomes European Sub 16156 A=0.96614 C=0.03386
gnomAD - Genomes African Sub 7969 A=0.3962 C=0.6038
gnomAD - Genomes American Sub 3139 A=0.8789 C=0.1211
gnomAD - Genomes East Asian Sub 773 A=0.999 C=0.001
gnomAD - Genomes Ashkenazi Jewish Sub 749 A=0.765 C=0.235
gnomAD - Genomes Other Sub 448 A=0.821 C=0.179
Allele Frequency Aggregator Total Global 28130 A=0.93228 C=0.06772
Allele Frequency Aggregator European Sub 26024 A=0.94655 C=0.05345
Allele Frequency Aggregator African Sub 714 A=0.454 C=0.546
Allele Frequency Aggregator Asian Sub 564 A=0.996 C=0.004
Allele Frequency Aggregator Other Sub 454 A=0.837 C=0.163
Allele Frequency Aggregator Latin American 2 Sub 140 A=0.943 C=0.057
Allele Frequency Aggregator Latin American 1 Sub 122 A=0.672 C=0.328
Allele Frequency Aggregator South Asian Sub 112 A=1.000 C=0.000
1000Genomes_30x Global Study-wide 1599 A=0.7361 C=0.2639
1000Genomes_30x African Sub 458 A=0.183 C=0.817
1000Genomes_30x South Asian Sub 319 A=1.000 C=0.000
1000Genomes_30x Europe Sub 305 A=0.970 C=0.030
1000Genomes_30x East Asian Sub 292 A=1.000 C=0.000
1000Genomes_30x American Sub 225 A=0.827 C=0.173
1000Genomes Global Study-wide 1233 A=0.7591 C=0.2409
1000Genomes African Sub 319 A=0.179 C=0.821
1000Genomes South Asian Sub 260 A=1.000 C=0.000
1000Genomes East Asian Sub 244 A=1.000 C=0.000
1000Genomes Europe Sub 240 A=0.975 C=0.025
1000Genomes American Sub 170 A=0.829 C=0.171
chrY_custom_capture Global Study-wide 896 A=0.908 C=0.092
chrY_custom_capture AFP Sub 0 A=0 C=0
chrY_custom_capture AHG Sub 0 A=0 C=0
chrY_custom_capture ASC Sub 0 A=0 C=0
chrY_custom_capture ASE Sub 0 A=0 C=0
chrY_custom_capture AUS Sub 0 A=0 C=0
chrY_custom_capture BRI Sub 0 A=0 C=0
chrY_custom_capture ENV Sub 0 A=0 C=0
chrY_custom_capture ESC Sub 0 A=0 C=0
chrY_custom_capture ESE Sub 0 A=0 C=0
chrY_custom_capture ESW Sub 0 A=0 C=0
chrY_custom_capture MEX Sub 0 A=0 C=0
chrY_custom_capture MNE Sub 0 A=0 C=0
chrY_custom_capture SCA Sub 0 A=0 C=0
Genome-wide autozygosity in Daghestan Global Study-wide 816 A=0.936 C=0.064
Genome-wide autozygosity in Daghestan Daghestan Sub 308 A=0.974 C=0.026
Genome-wide autozygosity in Daghestan Near_East Sub 144 A=0.806 C=0.194
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.984 C=0.016
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.889 C=0.111
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=1.00 C=0.00
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.94 C=0.06
Qatari Global Study-wide 53 A=0.89 C=0.11
SGDP_PRJ Global Study-wide 46 A=0.00 C=1.00
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 22 A=1.00 C=0.00
The Danish reference pan genome Danish Study-wide 20 A=0.90 C=0.10
Siberian Global Study-wide 2 A=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.11939602A>C
GRCh37.p13 chr Y NC_000024.9:g.14060308A>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 A= C
GRCh38.p14 chr Y NC_000024.10:g.11939602= NC_000024.10:g.11939602A>C
GRCh37.p13 chr Y NC_000024.9:g.14060308= NC_000024.9:g.14060308A>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#.

38 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23820025 Sep 20, 2004 (123)
2 ILLUMINA-UK ss115581680 Feb 06, 2009 (130)
3 BUSHMAN ss204417254 Jul 04, 2010 (132)
4 ILLUMINA ss536928506 Oct 12, 2018 (152)
5 TISHKOFF ss567113680 Apr 25, 2013 (138)
6 ILLUMINA ss778695910 Sep 08, 2015 (146)
7 CDBUSTAMANTE ss825682086 Aug 21, 2014 (142)
8 ILLUMINA ss834154738 Sep 08, 2015 (146)
9 HAMMER_LAB ss1397804165 Sep 08, 2015 (146)
10 JOBLING_UOL ss1399954866 Apr 01, 2015 (144)
11 1000GENOMES ss1556744115 Apr 01, 2015 (144)
12 EVA_GENOME_DK ss1583555416 Apr 01, 2015 (144)
13 WEILL_CORNELL_DGM ss1939859861 Feb 12, 2016 (147)
14 ILLUMINA ss1958175616 Feb 12, 2016 (147)
15 ILLUMINA ss1958175617 Feb 12, 2016 (147)
16 USC_VALOUEV ss2159351808 Dec 20, 2016 (150)
17 ILLUMINA ss2634993807 Nov 08, 2017 (151)
18 SWEGEN ss3020943868 Nov 08, 2017 (151)
19 ILLUMINA ss3023052746 Nov 08, 2017 (151)
20 ILLUMINA ss3023052747 Nov 08, 2017 (151)
21 HUMGEN ss3029946989 Nov 08, 2017 (151)
22 ILLUMINA ss3630504160 Oct 12, 2018 (152)
23 ILLUMINA ss3632876722 Oct 12, 2018 (152)
24 ILLUMINA ss3641265814 Oct 12, 2018 (152)
25 ILLUMINA ss3641564706 Oct 12, 2018 (152)
26 ILLUMINA ss3653611208 Oct 12, 2018 (152)
27 ILLUMINA ss3653611209 Oct 12, 2018 (152)
28 ILLUMINA ss3726713001 Jul 14, 2019 (153)
29 KHV_HUMAN_GENOMES ss3823534303 Jul 14, 2019 (153)
30 SGDP_PRJ ss3892696374 Apr 27, 2020 (154)
31 EVA ss3984771802 Apr 27, 2021 (155)
32 EVA ss3985985921 Apr 27, 2021 (155)
33 GNOMAD ss4126103775 Apr 27, 2021 (155)
34 EVA ss5237629807 Apr 27, 2021 (155)
35 ESTONIANBIOCENTRE ss5237680495 Oct 17, 2022 (156)
36 1000G_HIGH_COVERAGE ss5623810297 Oct 17, 2022 (156)
37 SANFORD_IMAGENETICS ss5666135064 Oct 17, 2022 (156)
38 EVA ss5848242292 Oct 17, 2022 (156)
39 1000Genomes NC_000024.9 - 14060308 Oct 12, 2018 (152)
40 1000Genomes_30x NC_000024.10 - 11939602 Oct 17, 2022 (156)
41 chrY_custom_capture NC_000024.9 - 14060308 Apr 27, 2020 (154)
42 Genome-wide autozygosity in Daghestan NC_000024.8 - 12570308 Apr 27, 2020 (154)
43 The Danish reference pan genome NC_000024.9 - 14060308 Apr 27, 2020 (154)
44 gnomAD - Genomes NC_000024.10 - 11939602 Apr 27, 2021 (155)
45 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 14060308 Apr 27, 2021 (155)
46 Qatari NC_000024.9 - 14060308 Apr 27, 2020 (154)
47 SGDP_PRJ NC_000024.9 - 14060308 Apr 27, 2020 (154)
48 Siberian NC_000024.9 - 14060308 Apr 27, 2020 (154)
49 ALFA NC_000024.10 - 11939602 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
555383, ss204417254, ss1397804165 NC_000024.8:12570307:A:C NC_000024.10:11939601:A:C (self)
84697103, 2141, 9720353, 1211848, 21901783, 44713354, 11868162, ss536928506, ss567113680, ss778695910, ss825682086, ss834154738, ss1399954866, ss1556744115, ss1583555416, ss1939859861, ss1958175616, ss1958175617, ss2159351808, ss2634993807, ss3020943868, ss3023052746, ss3023052747, ss3029946989, ss3630504160, ss3632876722, ss3641265814, ss3641564706, ss3653611208, ss3653611209, ss3892696374, ss3984771802, ss3985985921, ss5237629807, ss5237680495, ss5666135064, ss5848242292 NC_000024.9:14060307:A:C NC_000024.10:11939601:A:C (self)
111336232, 594937587, 2364434336, ss3726713001, ss3823534303, ss4126103775, ss5623810297 NC_000024.10:11939601:A:C NC_000024.10:11939601:A:C (self)
ss23820025, ss115581680 NT_011875.12:261729:A:C NC_000024.10:11939601:A: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 rs16980621

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