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dbSNP Short Genetic Variations

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.


Current Build 152

Released October 2, 2018

Homo sapiens
chr13:20189386 (GRCh38.p12) 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.

C>G / C>T
Variation Type
SNV Single Nucleotide Variation
T=0.00000 (1/246062, GnomAD)
T=0.00001 (1/125568, TOPMED)
T=0.0000 (1/30964, GnomAD)
Clinical Significance
Reported in ClinVar
Gene : Consequence
GJB2 : Missense Variant
2 citations
Genomic View
See rs on genome

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.p12 chr 13 NC_000013.11:g.20189386C>G
GRCh38.p12 chr 13 NC_000013.11:g.20189386C>T
GRCh37.p13 chr 13 NC_000013.10:g.20763525C>G
GRCh37.p13 chr 13 NC_000013.10:g.20763525C>T
GJB2 RefSeqGene NG_008358.1:g.8590G>C
GJB2 RefSeqGene NG_008358.1:g.8590G>A
Gene: GJB2, gap junction protein beta 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GJB2 transcript NM_004004.5:c.196G>C D [GAT] > H [CAT] Coding Sequence Variant
gap junction beta-2 protein NP_003995.2:p.Asp66His D (Asp) > H (His) Missense Variant
GJB2 transcript NM_004004.5:c.196G>A D [GAT] > N [AAT] Coding Sequence Variant
gap junction beta-2 protein NP_003995.2:p.Asp66Asn D (Asp) > N (Asn) Missense Variant
GJB2 transcript variant X1 XM_011535049.2:c.196G>C D [GAT] > H [CAT] Coding Sequence Variant
gap junction beta-2 protein isoform X1 XP_011533351.1:p.Asp66His D (Asp) > H (His) Missense Variant
GJB2 transcript variant X1 XM_011535049.2:c.196G>A D [GAT] > N [AAT] Coding Sequence Variant
gap junction beta-2 protein isoform X1 XP_011533351.1:p.Asp66Asn D (Asp) > N (Asn) Missense Variant

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: G (allele ID: 32051 )
ClinVar Accession Disease Names Clinical Significance
RCV000018536.30 Mutilating keratoderma Pathogenic

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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 246062 C=1.00000 T=0.00000
gnomAD - Exomes European Sub 133842 C=0.99999 T=0.00001
gnomAD - Exomes Asian Sub 48026 C=1.0000 T=0.0000
gnomAD - Exomes American Sub 33576 C=1.0000 T=0.0000
gnomAD - Exomes African Sub 15302 C=1.0000 T=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 9836 C=1.000 T=0.000
gnomAD - Exomes Other Sub 5480 C=1.000 T=0.000
TopMed Global Study-wide 125568 C=0.99999 T=0.00001
gnomAD - Genomes Global Study-wide 30964 C=1.0000 T=0.0000
gnomAD - Genomes European Sub 18494 C=1.0000 T=0.0000
gnomAD - Genomes African Sub 8728 C=1.000 T=0.000
gnomAD - Genomes East Asian Sub 1622 C=1.000 T=0.000
gnomAD - Genomes Other Sub 980 C=1.00 T=0.00
gnomAD - Genomes American Sub 838 C=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=1.00 T=0.00

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= G T Note
GRCh38.p12 chr 13 NC_000013.11:g.20...






GRCh37.p13 chr 13 NC_000013.10:g.20...






GJB2 RefSeqGene NG_008358.1:g.8590G= NG_008358.1:g.859...




GJB2 transcript NM_004004.5:c.196G= NM_004004.5:c.196G>C NM_004004.5:c.196G>A
GJB2 transcript variant X1 XM_011535049.2:c....






gap junction beta-2 protein NP_003995.2:p.Asp66= NP_003995.2:p.Asp...




gap junction beta-2 protein isoform X1 XP_011533351.1:p....







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#.

9 SubSNP, 3 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMICIA ss244239212 Aug 29, 2012 (137)
2 OMIM-CURATED-RECORDS ss275514330 Nov 22, 2010 (133)
3 ILLUMINA ss1959483755 Feb 12, 2016 (147)
4 GNOMAD ss2740301472 Nov 08, 2017 (151)
5 GNOMAD ss2749013740 Nov 08, 2017 (151)
6 GNOMAD ss2917235076 Nov 08, 2017 (151)
7 ILLUMINA ss3021487234 Nov 08, 2017 (151)
8 TOPMED ss3187174565 Nov 08, 2017 (151)
9 ILLUMINA ss3651871934 Oct 12, 2018 (152)
10 gnomAD - Genomes NC_000013.10 - 20763525 Oct 12, 2018 (152)
11 gnomAD - Exomes NC_000013.10 - 20763525 Oct 12, 2018 (152)
12 TopMed NC_000013.11 - 20189386 Oct 12, 2018 (152)
13 ClinVar RCV000018536.30 Oct 12, 2018 (152)

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
50936600, 7555129, ss1959483755, ss2740301472, ss2749013740, ss2917235076, ss3021487234, ss3651871934 NC_000013.10:20763524:C= NC_000013.11:20189385:C= (self)
96551326, ss244239212, ss275514330, ss3187174565 NC_000013.11:20189385:C= NC_000013.11:20189385:C= (self)
ss1959483755, ss3021487234, ss3651871934 NC_000013.10:20763524:C>G NC_000013.11:20189385:C>G (self)
RCV000018536.30, ss244239212, ss275514330 NC_000013.11:20189385:C>G NC_000013.11:20189385:C>G (self)
50936600, 7555129, ss2740301472, ss2749013740, ss2917235076 NC_000013.10:20763524:C>T NC_000013.11:20189385:C>T (self)
96551326, ss3187174565 NC_000013.11:20189385:C>T NC_000013.11:20189385:C>T (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs104894403
PMID Title Author Year Journal
9326398 Loricrin mutation in Vohwinkel's keratoderma is unique to the variant with ichthyosis. Korge BP et al. 1997 The Journal of investigative dermatology
10369869 A missense mutation in connexin26, D66H, causes mutilating keratoderma with sensorineural deafness (Vohwinkel's syndrome) in three unrelated families. Maestrini E et al. 1999 Human molecular genetics

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.post58+e54ea20