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NM_015404.4(WHRN):c.229A>T (p.Thr77Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(5);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Sep 30, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000045671.8
Variation ID:
45671
Description:
single nucleotide variant
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NM_015404.4(WHRN):c.229A>T (p.Thr77Ser)

Allele ID
54836
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q32
Genomic location
9: 114504573 (GRCh38) GRCh38 UCSC
9: 117266853 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.117266853T>A
NC_000009.12:g.114504573T>A
NG_016700.1:g.5884A>T
... more HGVS
Protein change
T77S
Other names
-
Canonical SPDI
NC_000009.12:114504572:T:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00699 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00519
The Genome Aggregation Database (gnomAD), exomes 0.00742
1000 Genomes Project 0.00699
Trans-Omics for Precision Medicine (TOPMed) 0.00617
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00792
Exome Aggregation Consortium (ExAC) 0.00783
Links
ClinGen: CA136910
dbSNP: rs56204273
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Jan 17, 2014 RCV000038889.5
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000514950.6
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001167578.1
Benign 1 criteria provided, single submitter Apr 27, 2017 RCV001167579.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
WHRN - - GRCh38
GRCh37
458 498

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 17, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000202617.7
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001950550.1
Submitted: (Sep 30, 2021)
Evidence details
Likely benign
(Aug 23, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000610911.1
Submitted: (Oct 05, 2017)
Evidence details
Benign
(May 15, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000062567.6
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (1)
Comment:
Thr77Ser in exon 1 of DFNB31: This variant has been reported in one individual w ith Usher syndrome (Aller 2010). However, it is not expected … (more)
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001113505.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 31
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001330096.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2D
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001330097.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sequence variants of the DFNB31 gene among Usher syndrome patients of diverse origin. Aller E Molecular vision 2010 PMID: 20352026
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=WHRN - - - -

Text-mined citations for rs56204273...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 20, 2021