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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.

rs2713395

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:15836799 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000023 (6/264690, TOPMED)
C=0.00005 (5/96240, GnomAD)
C=0.00011 (3/28254, 14KJPN) (+ 9 more)
C=0.00030 (5/16758, 8.3KJPN)
C=0.00012 (2/16324, ALFA)
C=0.0008 (5/6404, 1000G_30x)
C=0.0010 (3/2904, KOREAN)
C=0.0011 (2/1830, Korea1K)
C=0.000 (0/600, NorthernSweden)
C=0.000 (0/556, SGDP_PRJ)
C=0.000 (0/216, Qatari)
C=0.03 (1/40, 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 16324 C=0.00012 T=0.99988
European Sub 12072 C=0.00017 T=0.99983
African Sub 2816 C=0.0000 T=1.0000
African Others Sub 108 C=0.000 T=1.000
African American Sub 2708 C=0.0000 T=1.0000
Asian Sub 108 C=0.000 T=1.000
East Asian Sub 84 C=0.00 T=1.00
Other Asian Sub 24 C=0.00 T=1.00
Latin American 1 Sub 146 C=0.000 T=1.000
Latin American 2 Sub 610 C=0.000 T=1.000
South Asian Sub 94 C=0.00 T=1.00
Other Sub 478 C=0.000 T=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 C=0.000023 T=0.999977
gnomAD - Genomes Global Study-wide 96240 C=0.00005 T=0.99995
gnomAD - Genomes European Sub 56798 C=0.00004 T=0.99996
gnomAD - Genomes African Sub 24978 C=0.00012 T=0.99988
gnomAD - Genomes American Sub 8084 C=0.0000 T=1.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2652 C=0.0000 T=1.0000
gnomAD - Genomes East Asian Sub 2404 C=0.0000 T=1.0000
gnomAD - Genomes Other Sub 1324 C=0.0000 T=1.0000
14KJPN JAPANESE Study-wide 28254 C=0.00011 T=0.99989
8.3KJPN JAPANESE Study-wide 16758 C=0.00030 T=0.99970
Allele Frequency Aggregator Total Global 16324 C=0.00012 T=0.99988
Allele Frequency Aggregator European Sub 12072 C=0.00017 T=0.99983
Allele Frequency Aggregator African Sub 2816 C=0.0000 T=1.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.000 T=1.000
Allele Frequency Aggregator Other Sub 478 C=0.000 T=1.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.000 T=1.000
Allele Frequency Aggregator Asian Sub 108 C=0.000 T=1.000
Allele Frequency Aggregator South Asian Sub 94 C=0.00 T=1.00
1000Genomes_30x Global Study-wide 6404 C=0.0008 T=0.9992
1000Genomes_30x African Sub 1786 C=0.0011 T=0.9989
1000Genomes_30x Europe Sub 1266 C=0.0008 T=0.9992
1000Genomes_30x South Asian Sub 1202 C=0.0017 T=0.9983
1000Genomes_30x East Asian Sub 1170 C=0.0000 T=1.0000
1000Genomes_30x American Sub 980 C=0.000 T=1.000
KOREAN population from KRGDB KOREAN Study-wide 2904 C=0.0010 T=0.9990
Korean Genome Project KOREAN Study-wide 1830 C=0.0011 T=0.9989
Northern Sweden ACPOP Study-wide 600 C=0.000 T=1.000
SGDP_PRJ Global Study-wide 556 C=0.000 T=1.000
Qatari Global Study-wide 216 C=0.000 T=1.000
The Danish reference pan genome Danish Study-wide 40 C=0.03 T=0.97
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 22 NC_000022.11:g.15836799C>T
GRCh37.p13 chr 22 NC_000022.10:g.16141164G>A
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 C= T
GRCh38.p14 chr 22 NC_000022.11:g.15836799= NC_000022.11:g.15836799C>T
GRCh37.p13 chr 22 NC_000022.10:g.16141164= NC_000022.10:g.16141164G>A
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#.

37 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3833819 Sep 28, 2001 (100)
2 TSC-CSHL ss5409301 Oct 10, 2002 (110)
3 SC_SNP ss7991179 Apr 21, 2003 (114)
4 BCM_SSAHASNP ss11001777 Jul 11, 2003 (116)
5 WI_SSAHASNP ss12525410 Jul 11, 2003 (116)
6 WUGSC_SSAHASNP ss14534413 Dec 05, 2003 (119)
7 HGSV ss84433293 Dec 15, 2007 (142)
8 HUMANGENOME_JCVI ss96091316 Feb 04, 2009 (142)
9 GMI ss283570018 May 04, 2012 (137)
10 PJP ss292731331 May 09, 2011 (134)
11 1000GENOMES ss341066113 May 09, 2011 (134)
12 SSMP ss662459692 Apr 25, 2013 (138)
13 DDI ss1429209510 Apr 01, 2015 (144)
14 EVA_GENOME_DK ss1579693850 Apr 01, 2015 (144)
15 WEILL_CORNELL_DGM ss1938751107 Feb 12, 2016 (147)
16 JJLAB ss2030150085 Sep 14, 2016 (149)
17 GRF ss2704489335 Nov 08, 2017 (151)
18 GNOMAD ss2972611882 Nov 08, 2017 (151)
19 SWEGEN ss3019015872 Nov 08, 2017 (151)
20 CSHL ss3352757655 Nov 08, 2017 (151)
21 URBANLAB ss3651142616 Oct 12, 2018 (152)
22 ACPOP ss3743799347 Jul 13, 2019 (153)
23 EVA ss3835914950 Apr 27, 2020 (154)
24 EVA ss3841585465 Apr 27, 2020 (154)
25 EVA ss3847099241 Apr 27, 2020 (154)
26 SGDP_PRJ ss3890174087 Apr 27, 2020 (154)
27 KRGDB ss3940532426 Apr 27, 2020 (154)
28 KOGIC ss3983318714 Apr 27, 2020 (154)
29 TOPMED ss5104205982 Apr 26, 2021 (155)
30 TOMMO_GENOMICS ss5231875825 Apr 26, 2021 (155)
31 1000G_HIGH_COVERAGE ss5310550410 Oct 13, 2022 (156)
32 1000G_HIGH_COVERAGE ss5617858063 Oct 13, 2022 (156)
33 SANFORD_IMAGENETICS ss5664166205 Oct 13, 2022 (156)
34 TOMMO_GENOMICS ss5792767787 Oct 13, 2022 (156)
35 YY_MCH ss5818560442 Oct 13, 2022 (156)
36 EVA ss5821860310 Oct 13, 2022 (156)
37 EVA ss5959063525 Oct 13, 2022 (156)
38 1000Genomes_30x NC_000022.11 - 15836799 Oct 13, 2022 (156)
39 The Danish reference pan genome NC_000022.10 - 16141164 Apr 27, 2020 (154)
40 gnomAD - Genomes NC_000022.11 - 15836799 Apr 26, 2021 (155)
41 KOREAN population from KRGDB NC_000022.10 - 16141164 Apr 27, 2020 (154)
42 Korean Genome Project NC_000022.11 - 15836799 Apr 27, 2020 (154)
43 Northern Sweden NC_000022.10 - 16141164 Jul 13, 2019 (153)
44 Qatari NC_000022.10 - 16141164 Apr 27, 2020 (154)
45 SGDP_PRJ NC_000022.10 - 16141164 Apr 27, 2020 (154)
46 8.3KJPN NC_000022.10 - 16141164 Apr 26, 2021 (155)
47 14KJPN NC_000022.11 - 15836799 Oct 13, 2022 (156)
48 TopMed NC_000022.11 - 15836799 Apr 26, 2021 (155)
49 ALFA NC_000022.11 - 15836799 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)
rs4047093 Dec 16, 2002 (110)
rs60472239 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84433293 NC_000022.8:14521163:G:A NC_000022.11:15836798:C:T (self)
ss283570018, ss292731331 NC_000022.9:14521163:G:A NC_000022.11:15836798:C:T (self)
5858789, 47709820, 17084212, 20793029, 42191067, 89845132, ss341066113, ss662459692, ss1429209510, ss1579693850, ss1938751107, ss2030150085, ss2704489335, ss2972611882, ss3019015872, ss3352757655, ss3743799347, ss3835914950, ss3841585465, ss3890174087, ss3940532426, ss5231875825, ss5664166205, ss5821860310, ss5959063525 NC_000022.10:16141163:G:A NC_000022.11:15836798:C:T (self)
105383998, 565718692, 39696715, 126604891, 379314929, 11435460469, ss3651142616, ss3847099241, ss3983318714, ss5104205982, ss5310550410, ss5617858063, ss5792767787, ss5818560442 NC_000022.11:15836798:C:T NC_000022.11:15836798:C:T (self)
ss7991179, ss11001777, ss12525410, ss14534413 NT_011516.5:91163:G:A NC_000022.11:15836798:C:T (self)
ss3833819, ss5409301, ss96091316 NT_028395.3:91163:G:A NC_000022.11:15836798:C: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 rs2713395

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