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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.

rs199524735

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:43609293 (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=0.000859 (215/250252, GnomAD_exome)
C=0.003348 (463/138284, GnomAD)
C=0.000521 (63/120986, ExAC) (+ 5 more)
C=0.00089 (25/28096, 14KJPN)
C=0.00166 (42/25320, ALFA)
C=0.00096 (16/16648, 8.3KJPN)
C=0.0072 (46/6404, 1000G_30x)
A=0.3 (2/6, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
STRC : Synonymous Variant
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 25320 A=0.99834 C=0.00166
European Sub 18142 A=0.99906 C=0.00094
African Sub 3410 A=0.9950 C=0.0050
African Others Sub 116 A=0.991 C=0.009
African American Sub 3294 A=0.9951 C=0.0049
Asian Sub 164 A=1.000 C=0.000
East Asian Sub 110 A=1.000 C=0.000
Other Asian Sub 54 A=1.00 C=0.00
Latin American 1 Sub 146 A=0.993 C=0.007
Latin American 2 Sub 610 A=0.998 C=0.002
South Asian Sub 94 A=0.99 C=0.01
Other Sub 2754 A=0.9982 C=0.0018


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 - Exomes Global Study-wide 250252 A=0.999141 C=0.000859
gnomAD - Exomes European Sub 134992 A=0.999770 C=0.000230
gnomAD - Exomes Asian Sub 48648 A=0.99858 C=0.00142
gnomAD - Exomes American Sub 34516 A=0.99841 C=0.00159
gnomAD - Exomes African Sub 15910 A=0.99679 C=0.00321
gnomAD - Exomes Ashkenazi Jewish Sub 10064 A=0.99950 C=0.00050
gnomAD - Exomes Other Sub 6122 A=0.9993 C=0.0007
gnomAD - Genomes Global Study-wide 138284 A=0.996652 C=0.003348
gnomAD - Genomes European Sub 75872 A=0.99922 C=0.00078
gnomAD - Genomes African Sub 40290 A=0.99275 C=0.00725
gnomAD - Genomes American Sub 13588 A=0.99330 C=0.00670
gnomAD - Genomes Ashkenazi Jewish Sub 3316 A=0.9988 C=0.0012
gnomAD - Genomes East Asian Sub 3080 A=0.9977 C=0.0023
gnomAD - Genomes Other Sub 2138 A=0.9953 C=0.0047
ExAC Global Study-wide 120986 A=0.999479 C=0.000521
ExAC Europe Sub 73316 A=0.99978 C=0.00022
ExAC Asian Sub 25012 A=0.99952 C=0.00048
ExAC American Sub 11564 A=0.99965 C=0.00035
ExAC African Sub 10186 A=0.99696 C=0.00304
ExAC Other Sub 908 A=1.000 C=0.000
14KJPN JAPANESE Study-wide 28096 A=0.99911 C=0.00089
Allele Frequency Aggregator Total Global 25320 A=0.99834 C=0.00166
Allele Frequency Aggregator European Sub 18142 A=0.99906 C=0.00094
Allele Frequency Aggregator African Sub 3410 A=0.9950 C=0.0050
Allele Frequency Aggregator Other Sub 2754 A=0.9982 C=0.0018
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.998 C=0.002
Allele Frequency Aggregator Asian Sub 164 A=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.993 C=0.007
Allele Frequency Aggregator South Asian Sub 94 A=0.99 C=0.01
8.3KJPN JAPANESE Study-wide 16648 A=0.99904 C=0.00096
1000Genomes_30x Global Study-wide 6404 A=0.9928 C=0.0072
1000Genomes_30x African Sub 1786 A=0.9871 C=0.0129
1000Genomes_30x Europe Sub 1266 A=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 A=0.9900 C=0.0100
1000Genomes_30x East Asian Sub 1170 A=0.9957 C=0.0043
1000Genomes_30x American Sub 980 A=0.994 C=0.006
SGDP_PRJ Global Study-wide 6 A=0.3 C=0.7
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 15 NC_000015.10:g.43609293A>C
GRCh37.p13 chr 15 NC_000015.9:g.43901491A>C
STRC RefSeqGene NG_011636.1:g.14508T>G
Gene: STRC, stereocilin (minus strand)
Molecule type Change Amino acid[Codon] SO Term
STRC transcript NM_153700.2:c.3540T>G L [CTT] > L [CTG] Coding Sequence Variant
stereocilin precursor NP_714544.1:p.Leu1180= L (Leu) > L (Leu) Synonymous Variant
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.

Allele: C (allele ID: 230570 )
ClinVar Accession Disease Names Clinical Significance
RCV000217415.6 not specified Benign
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 15 NC_000015.10:g.43609293= NC_000015.10:g.43609293A>C
GRCh37.p13 chr 15 NC_000015.9:g.43901491= NC_000015.9:g.43901491A>C
STRC RefSeqGene NG_011636.1:g.14508= NG_011636.1:g.14508T>G
STRC transcript NM_153700.2:c.3540= NM_153700.2:c.3540T>G
stereocilin precursor NP_714544.1:p.Leu1180= NP_714544.1:p.Leu1180=
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#.

19 SubSNP, 8 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ENSEMBL ss142914621 Jul 19, 2016 (147)
2 CLINSEQ_SNP ss491699718 May 04, 2012 (137)
3 EVA_EXAC ss1691800494 Apr 01, 2015 (144)
4 SYSTEMSBIOZJU ss2628667319 Nov 08, 2017 (151)
5 GNOMAD ss2741201141 Nov 08, 2017 (151)
6 GNOMAD ss2749292047 Nov 08, 2017 (151)
7 GNOMAD ss2934237218 Nov 08, 2017 (151)
8 SWEGEN ss3013189866 Nov 08, 2017 (151)
9 SGDP_PRJ ss3882798296 Apr 27, 2020 (154)
10 EVA ss3986646030 Apr 27, 2021 (155)
11 TOMMO_GENOMICS ss5215924255 Apr 27, 2021 (155)
12 1000G_HIGH_COVERAGE ss5298242308 Oct 16, 2022 (156)
13 TRAN_CS_UWATERLOO ss5314440974 Oct 16, 2022 (156)
14 EVA ss5418871283 Oct 16, 2022 (156)
15 1000G_HIGH_COVERAGE ss5599542747 Oct 16, 2022 (156)
16 EVA ss5624052523 Oct 16, 2022 (156)
17 SANFORD_IMAGENETICS ss5657396886 Oct 16, 2022 (156)
18 TOMMO_GENOMICS ss5769650705 Oct 16, 2022 (156)
19 EVA ss5875649923 Oct 16, 2022 (156)
20 1000Genomes_30x NC_000015.10 - 43609293 Oct 16, 2022 (156)
21 ExAC NC_000015.9 - 43901491 Oct 12, 2018 (152)
22 gnomAD - Genomes NC_000015.10 - 43609293 Apr 27, 2021 (155)
23 gnomAD - Exomes NC_000015.9 - 43901491 Jul 13, 2019 (153)
24 SGDP_PRJ NC_000015.9 - 43901491 Apr 27, 2020 (154)
25 8.3KJPN NC_000015.9 - 43901491 Apr 27, 2021 (155)
26 14KJPN NC_000015.10 - 43609293 Oct 16, 2022 (156)
27 ALFA NC_000015.10 - 43609293 Apr 27, 2021 (155)
28 ClinVar RCV000217415.6 Oct 16, 2022 (156)
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
ss491699718 NC_000015.8:41688782:A:C NC_000015.10:43609292:A:C (self)
2171803, 10465533, 34815276, 73893562, ss1691800494, ss2628667319, ss2741201141, ss2749292047, ss2934237218, ss3013189866, ss3882798296, ss3986646030, ss5215924255, ss5418871283, ss5624052523, ss5657396886 NC_000015.9:43901490:A:C NC_000015.10:43609292:A:C (self)
RCV000217415.6, 87068682, 467369296, 103487809, 5786811636, ss5298242308, ss5314440974, ss5599542747, ss5769650705, ss5875649923 NC_000015.10:43609292:A:C NC_000015.10:43609292:A:C (self)
ss142914621 NT_010194.17:14692047:A:C NC_000015.10:43609292: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.

1 citation for rs199524735
PMID Title Author Year Journal
24033266 A systematic approach to assessing the clinical significance of genetic variants. Duzkale H et al. 2013 Clinical genetics
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