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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.

rs767044398

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:20222983 (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
T=0.000004 (1/264690, TOPMED)
T=0.000016 (4/251490, GnomAD_exome)
T=0.000014 (2/140236, GnomAD) (+ 2 more)
T=0.000016 (2/121402, ExAC)
T=0.00005 (1/19668, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GJB6 : 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 36030 C=0.99994 T=0.00006
European Sub 23114 C=0.99991 T=0.00009
African Sub 7726 C=1.0000 T=0.0000
African Others Sub 276 C=1.000 T=0.000
African American Sub 7450 C=1.0000 T=0.0000
Asian Sub 164 C=1.000 T=0.000
East Asian Sub 110 C=1.000 T=0.000
Other Asian Sub 54 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 94 C=1.00 T=0.00
Other Sub 4176 C=1.0000 T=0.0000


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=0.999996 T=0.000004
gnomAD - Exomes Global Study-wide 251490 C=0.999984 T=0.000016
gnomAD - Exomes European Sub 135414 C=0.999970 T=0.000030
gnomAD - Exomes Asian Sub 49010 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34590 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16256 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6140 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140236 C=0.999986 T=0.000014
gnomAD - Genomes European Sub 75940 C=0.99997 T=0.00003
gnomAD - Genomes African Sub 42034 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13660 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2148 C=1.0000 T=0.0000
ExAC Global Study-wide 121402 C=0.999984 T=0.000016
ExAC Europe Sub 73350 C=0.99997 T=0.00003
ExAC Asian Sub 25166 C=1.00000 T=0.00000
ExAC American Sub 11574 C=1.00000 T=0.00000
ExAC African Sub 10404 C=1.00000 T=0.00000
ExAC Other Sub 908 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 19668 C=0.99995 T=0.00005
Allele Frequency Aggregator European Sub 13024 C=0.99992 T=0.00008
Allele Frequency Aggregator African Sub 2888 C=1.0000 T=0.0000
Allele Frequency Aggregator Other Sub 2742 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 164 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 T=0.00
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 13 NC_000013.11:g.20222983C>T
GRCh37.p13 chr 13 NC_000013.10:g.20797122C>T
GJB6 RefSeqGene (LRG_1395) NG_008323.1:g.14413G>A
Gene: GJB6, gap junction protein beta 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GJB6 transcript variant 1 NM_001110219.3:c.498G>A V [GTG] > V [GTA] Coding Sequence Variant
gap junction beta-6 protein NP_001103689.1:p.Val166= V (Val) > V (Val) Synonymous Variant
GJB6 transcript variant 6 NM_001370091.1:c.498G>A V [GTG] > V [GTA] Coding Sequence Variant
gap junction beta-6 protein NP_001357020.1:p.Val166= V (Val) > V (Val) Synonymous Variant
GJB6 transcript variant 7 NM_001370092.1:c.498G>A V [GTG] > V [GTA] Coding Sequence Variant
gap junction beta-6 protein NP_001357021.1:p.Val166= V (Val) > V (Val) Synonymous Variant
GJB6 transcript variant 5 NM_001370090.1:c.498G>A V [GTG] > V [GTA] Coding Sequence Variant
gap junction beta-6 protein NP_001357019.1:p.Val166= V (Val) > V (Val) Synonymous Variant
GJB6 transcript variant 3 NM_006783.5:c.498G>A V [GTG] > V [GTA] Coding Sequence Variant
gap junction beta-6 protein NP_006774.2:p.Val166= V (Val) > V (Val) Synonymous Variant
GJB6 transcript variant 2 NM_001110220.3:c.498G>A V [GTG] > V [GTA] Coding Sequence Variant
gap junction beta-6 protein NP_001103690.1:p.Val166= V (Val) > V (Val) Synonymous Variant
GJB6 transcript variant 4 NM_001110221.3:c.498G>A V [GTG] > V [GTA] Coding Sequence Variant
gap junction beta-6 protein NP_001103691.1:p.Val166= V (Val) > V (Val) Synonymous Variant
GJB6 transcript variant X1 XM_047430056.1:c.498G>A V [GTG] > V [GTA] Coding Sequence Variant
gap junction beta-6 protein isoform X1 XP_047286012.1:p.Val166= V (Val) > V (Val) Synonymous Variant
GJB6 transcript variant X2 XM_047430057.1:c.498G>A V [GTG] > V [GTA] Coding Sequence Variant
gap junction beta-6 protein isoform X1 XP_047286013.1:p.Val166= V (Val) > V (Val) 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.

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 13 NC_000013.11:g.20222983= NC_000013.11:g.20222983C>T
GRCh37.p13 chr 13 NC_000013.10:g.20797122= NC_000013.10:g.20797122C>T
GJB6 RefSeqGene (LRG_1395) NG_008323.1:g.14413= NG_008323.1:g.14413G>A
GJB6 transcript variant 3 NM_006783.5:c.498= NM_006783.5:c.498G>A
GJB6 transcript variant 3 NM_006783.4:c.498= NM_006783.4:c.498G>A
GJB6 transcript variant 1 NM_001110219.3:c.498= NM_001110219.3:c.498G>A
GJB6 transcript variant 1 NM_001110219.2:c.498= NM_001110219.2:c.498G>A
GJB6 transcript variant 2 NM_001110220.3:c.498= NM_001110220.3:c.498G>A
GJB6 transcript variant 2 NM_001110220.2:c.498= NM_001110220.2:c.498G>A
GJB6 transcript variant 4 NM_001110221.3:c.498= NM_001110221.3:c.498G>A
GJB6 transcript variant 4 NM_001110221.2:c.498= NM_001110221.2:c.498G>A
GJB6 transcript variant 7 NM_001370092.1:c.498= NM_001370092.1:c.498G>A
GJB6 transcript variant 5 NM_001370090.1:c.498= NM_001370090.1:c.498G>A
GJB6 transcript variant 6 NM_001370091.1:c.498= NM_001370091.1:c.498G>A
GJB6 transcript variant X1 XM_047430056.1:c.498= XM_047430056.1:c.498G>A
GJB6 transcript variant X2 XM_047430057.1:c.498= XM_047430057.1:c.498G>A
gap junction beta-6 protein NP_006774.2:p.Val166= NP_006774.2:p.Val166=
gap junction beta-6 protein NP_001103689.1:p.Val166= NP_001103689.1:p.Val166=
gap junction beta-6 protein NP_001103690.1:p.Val166= NP_001103690.1:p.Val166=
gap junction beta-6 protein NP_001103691.1:p.Val166= NP_001103691.1:p.Val166=
gap junction beta-6 protein NP_001357021.1:p.Val166= NP_001357021.1:p.Val166=
gap junction beta-6 protein NP_001357019.1:p.Val166= NP_001357019.1:p.Val166=
gap junction beta-6 protein NP_001357020.1:p.Val166= NP_001357020.1:p.Val166=
gap junction beta-6 protein isoform X1 XP_047286012.1:p.Val166= XP_047286012.1:p.Val166=
gap junction beta-6 protein isoform X1 XP_047286013.1:p.Val166= XP_047286013.1:p.Val166=
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#.

5 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1691217171 Apr 01, 2015 (144)
2 CLINVAR ss1751113503 May 21, 2015 (136)
3 GNOMAD ss2740301636 Nov 08, 2017 (151)
4 GNOMAD ss4262205138 Apr 26, 2021 (155)
5 TOPMED ss4938872616 Apr 26, 2021 (155)
6 ExAC NC_000013.10 - 20797122 Oct 12, 2018 (152)
7 gnomAD - Genomes NC_000013.11 - 20222983 Apr 26, 2021 (155)
8 gnomAD - Exomes NC_000013.10 - 20797122 Jul 13, 2019 (153)
9 TopMed NC_000013.11 - 20222983 Apr 26, 2021 (155)
10 ALFA NC_000013.11 - 20222983 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)
rs786204306 Jun 25, 2015 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
1539930, 9542862, ss1691217171, ss2740301636 NC_000013.10:20797121:C:T NC_000013.11:20222982:C:T (self)
424604352, 154418274, 11031837581, ss1751113503, ss4262205138, ss4938872616 NC_000013.11:20222982:C:T NC_000013.11:20222982: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.

1 citation for rs767044398
PMID Title Author Year Journal
18414213 ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Richards CS et al. 2008 Genetics in medicine
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