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NM_015404.4(WHRN):c.1678G>A (p.Ala560Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 5, 2020
Accession:
VCV000163047.4
Variation ID:
163047
Description:
single nucleotide variant
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NM_015404.4(WHRN):c.1678G>A (p.Ala560Thr)

Allele ID
174822
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q32
Genomic location
9: 114407967 (GRCh38) GRCh38 UCSC
9: 117170247 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.117170247C>T
NC_000009.12:g.114407967C>T
NM_015404.4:c.1678G>A MANE Select NP_056219.3:p.Ala560Thr missense
... more HGVS
Protein change
A560T, A177T, A209T
Other names
-
Canonical SPDI
NC_000009.12:114407966:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00083
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00021
Exome Aggregation Consortium (ExAC) 0.00051
The Genome Aggregation Database (gnomAD), exomes 0.00039
Links
ClinGen: CA175636
dbSNP: rs182072601
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter May 13, 2014 RCV000150389.1
Uncertain significance 1 criteria provided, single submitter Oct 5, 2020 RCV001204350.2
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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
437 477

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(May 13, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000197550.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Ala560Thr variant in exon 8 of DFNB31: This variant is not expected to have clin ical significance due to a lack of conservation across species, … (more)
Uncertain significance
(Oct 05, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001375552.2
Submitted: (Jan 07, 2021)
Evidence details
Comment:
This sequence change replaces alanine with threonine at codon 560 of the WHRN protein (p.Ala560Thr). The alanine residue is weakly conserved and there is a … (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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs182072601...

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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 Jul 07, 2021