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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.

rs757774496

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr12:80279038 (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.

Alleles
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00003 (8/230928, GnomAD)
T=0.00005 (6/125568, TOPMED)
T=0.00001 (1/118216, ExAC) (+ 1 more)
T=0.0000 (1/30850, GnomAD)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OTOGL : Stop Gained
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 12 NC_000012.12:g.80279038C>A
GRCh38.p12 chr 12 NC_000012.12:g.80279038C>T
GRCh37.p13 chr 12 NC_000012.11:g.80672818C>A
GRCh37.p13 chr 12 NC_000012.11:g.80672818C>T
OTOGL RefSeqGene NG_033008.1:g.74586C>A
OTOGL RefSeqGene NG_033008.1:g.74586C>T
Gene: OTOGL, otogelin like (plus strand)
Molecule type Change Amino acid[Codon] SO Term
OTOGL transcript variant 1 NM_173591.3:c.2773C>A R [CGA] > R [AGA] Coding Sequence Variant
otogelin-like protein isoform 1 precursor NP_775862.3:p.Arg925= R (Arg) > R (Arg) Synonymous Variant
OTOGL transcript variant 1 NM_173591.3:c.2773C>T R [CGA] > * [TGA] Coding Sequence Variant
otogelin-like protein isoform 1 precursor NP_775862.3:p.Arg925Ter R (Arg) > * (Ter) Stop Gained
OTOGL transcript variant X2 XM_011538191.1:c.2824C>A R [CGA] > R [AGA] Coding Sequence Variant
otogelin-like protein isoform X2 XP_011536493.1:p.Arg942= R (Arg) > R (Arg) Synonymous Variant
OTOGL transcript variant X2 XM_011538191.1:c.2824C>T R [CGA] > * [TGA] Coding Sequence Variant
otogelin-like protein isoform X2 XP_011536493.1:p.Arg942Ter R (Arg) > * (Ter) Stop Gained
OTOGL transcript variant X4 XM_011538193.1:c.2458C>A R [CGA] > R [AGA] Coding Sequence Variant
otogelin-like protein isoform X4 XP_011536495.1:p.Arg820= R (Arg) > R (Arg) Synonymous Variant
OTOGL transcript variant X4 XM_011538193.1:c.2458C>T R [CGA] > * [TGA] Coding Sequence Variant
otogelin-like protein isoform X4 XP_011536495.1:p.Arg820Ter R (Arg) > * (Ter) Stop Gained
OTOGL transcript variant X1 XM_005268802.3:c.2824C>A R [CGA] > R [AGA] Coding Sequence Variant
otogelin-like protein isoform X1 XP_005268859.1:p.Arg942= R (Arg) > R (Arg) Synonymous Variant
OTOGL transcript variant X1 XM_005268802.3:c.2824C>T R [CGA] > * [TGA] Coding Sequence Variant
otogelin-like protein isoform X1 XP_005268859.1:p.Arg942Ter R (Arg) > * (Ter) Stop Gained
OTOGL transcript variant X3 XM_011538192.2:c.2671C>A R [CGA] > R [AGA] Coding Sequence Variant
otogelin-like protein isoform X3 XP_011536494.1:p.Arg891= R (Arg) > R (Arg) Synonymous Variant
OTOGL transcript variant X3 XM_011538192.2:c.2671C>T R [CGA] > * [TGA] Coding Sequence Variant
otogelin-like protein isoform X3 XP_011536494.1:p.Arg891Ter R (Arg) > * (Ter) Stop Gained
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

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 230928 C=0.99997 T=0.00003
gnomAD - Exomes European Sub 120318 C=0.99995 T=0.00005
gnomAD - Exomes Asian Sub 47412 C=1.0000 T=0.0000
gnomAD - Exomes American Sub 33228 C=1.0000 T=0.0000
gnomAD - Exomes African Sub 14884 C=1.0000 T=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 9764 C=1.000 T=0.000
gnomAD - Exomes Other Sub 5322 C=1.000 T=0.000
TopMed Global Study-wide 125568 C=0.99995 T=0.00005
ExAC Global Study-wide 118216 C=0.99999 T=0.00001
ExAC Europe Sub 71808 C=1.0000 T=0.0000
ExAC Asian Sub 24790 C=1.0000 T=0.0000
ExAC American Sub 11296 C=1.0000 T=0.0000
ExAC African Sub 9446 C=1.000 T=0.000
ExAC Other Sub 876 C=1.00 T=0.00
gnomAD - Genomes Global Study-wide 30850 C=1.0000 T=0.0000
gnomAD - Genomes European Sub 18432 C=0.9999 T=0.0001
gnomAD - Genomes African Sub 8720 C=1.000 T=0.000
gnomAD - Genomes East Asian Sub 1582 C=1.000 T=0.000
gnomAD - Genomes Other Sub 980 C=1.00 T=0.00
gnomAD - Genomes American Sub 834 C=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=1.00 T=0.00
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= A T Note
GRCh38.p12 chr 12 NC_000012.12:g.80...

NC_000012.12:g.80279038C=

NC_000012.12:g.80...

NC_000012.12:g.80279038C>A

NC_000012.12:g.80...

NC_000012.12:g.80279038C>T

GRCh37.p13 chr 12 NC_000012.11:g.80...

NC_000012.11:g.80672818C=

NC_000012.11:g.80...

NC_000012.11:g.80672818C>A

NC_000012.11:g.80...

NC_000012.11:g.80672818C>T

OTOGL RefSeqGene NG_033008.1:g.745...

NG_033008.1:g.74586C=

NG_033008.1:g.745...

NG_033008.1:g.74586C>A

NG_033008.1:g.745...

NG_033008.1:g.74586C>T

OTOGL transcript variant 1 NM_173591.3:c.2773C= NM_173591.3:c.277...

NM_173591.3:c.2773C>A

NM_173591.3:c.277...

NM_173591.3:c.2773C>T

OTOGL transcript variant X1 XM_005268802.3:c....

XM_005268802.3:c.2824C=

XM_005268802.3:c....

XM_005268802.3:c.2824C>A

XM_005268802.3:c....

XM_005268802.3:c.2824C>T

OTOGL transcript variant X1 XM_005268802.1:c....

XM_005268802.1:c.2824C=

XM_005268802.1:c....

XM_005268802.1:c.2824C>A

XM_005268802.1:c....

XM_005268802.1:c.2824C>T

OTOGL transcript variant X3 XM_011538192.2:c....

XM_011538192.2:c.2671C=

XM_011538192.2:c....

XM_011538192.2:c.2671C>A

XM_011538192.2:c....

XM_011538192.2:c.2671C>T

OTOGL transcript variant X2 XM_011538191.1:c....

XM_011538191.1:c.2824C=

XM_011538191.1:c....

XM_011538191.1:c.2824C>A

XM_011538191.1:c....

XM_011538191.1:c.2824C>T

OTOGL transcript variant X4 XM_011538193.1:c....

XM_011538193.1:c.2458C=

XM_011538193.1:c....

XM_011538193.1:c.2458C>A

XM_011538193.1:c....

XM_011538193.1:c.2458C>T

otogelin-like protein isoform 1 precursor NP_775862.3:p.Arg...

NP_775862.3:p.Arg925=

NP_775862.3:p.Arg...

NP_775862.3:p.Arg925=

NP_775862.3:p.Arg...

NP_775862.3:p.Arg925Ter

otogelin-like protein isoform X1 XP_005268859.1:p....

XP_005268859.1:p.Arg942=

XP_005268859.1:p....

XP_005268859.1:p.Arg942=

XP_005268859.1:p....

XP_005268859.1:p.Arg942Ter

otogelin-like protein isoform X3 XP_011536494.1:p....

XP_011536494.1:p.Arg891=

XP_011536494.1:p....

XP_011536494.1:p.Arg891=

XP_011536494.1:p....

XP_011536494.1:p.Arg891Ter

otogelin-like protein isoform X2 XP_011536493.1:p....

XP_011536493.1:p.Arg942=

XP_011536493.1:p....

XP_011536493.1:p.Arg942=

XP_011536493.1:p....

XP_011536493.1:p.Arg942Ter

otogelin-like protein isoform X4 XP_011536495.1:p....

XP_011536495.1:p.Arg820=

XP_011536495.1:p....

XP_011536495.1:p.Arg820=

XP_011536495.1:p....

XP_011536495.1:p.Arg820Ter

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#.

9 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1691028466 Apr 01, 2015 (144)
2 HUMAN_LONGEVITY ss2191421323 Dec 20, 2016 (150)
3 TOPMED ss2355415382 Dec 20, 2016 (150)
4 GNOMAD ss2740004928 Nov 08, 2017 (151)
5 GNOMAD ss2748922516 Nov 08, 2017 (151)
6 GNOMAD ss2912782913 Nov 08, 2017 (151)
7 ILLUMINA ss3021448214 Nov 08, 2017 (151)
8 TOPMED ss3176132425 Nov 08, 2017 (151)
9 ILLUMINA ss3651829172 Oct 12, 2018 (152)
10 ExAC NC_000012.11 - 80672818 Oct 12, 2018 (152)
11 gnomAD - Genomes NC_000012.11 - 80672818 Oct 12, 2018 (152)
12 gnomAD - Exomes NC_000012.11 - 80672818 Oct 12, 2018 (152)
13 TopMed NC_000012.12 - 80279038 Oct 12, 2018 (152)
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
ss2191421323 NC_000012.12:80279037:C:A NC_000012.12:80279037:C:A (self)
1335355, 46484436, 7316379, ss1691028466, ss2355415382, ss2740004928, ss2748922516, ss2912782913, ss3021448214, ss3651829172 NC_000012.11:80672817:C:T NC_000012.12:80279037:C:T (self)
88157407, ss2191421323, ss3176132425 NC_000012.12:80279037:C:T NC_000012.12:80279037: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 rs757774496

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.post104+4a6ee9c