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NM_015404.4(WHRN):c.1887G>A (p.Pro629=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 30, 2020
Accession:
VCV000227290.7
Variation ID:
227290
Description:
single nucleotide variant
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NM_015404.4(WHRN):c.1887G>A (p.Pro629=)

Allele ID
229651
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q32
Genomic location
9: 114406704 (GRCh38) GRCh38 UCSC
9: 117168984 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.117168984C>T
NC_000009.12:g.114406704C>T
NM_015404.4:c.1887G>A MANE Select NP_056219.3:p.Pro629= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000009.12:114406703:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00025
Exome Aggregation Consortium (ExAC) 0.00024
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
The Genome Aggregation Database (gnomAD) 0.00019
1000 Genomes Project 0.00060
Trans-Omics for Precision Medicine (TOPMed) 0.00032
Links
ClinGen: CA5205788
dbSNP: rs143443833
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Oct 30, 2020 RCV000965116.4
Likely benign 1 criteria provided, single submitter Jan 13, 2017 RCV000219020.2
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000321890.2
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000360251.2
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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
447 487

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 13, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000270104.3
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Pro629Pro in Exon 09 of DFNB31: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is … (more)
Benign
(Feb 25, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143728.1
Submitted: (Sep 25, 2019)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 31
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000476752.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2D
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000476753.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Oct 30, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001112373.3
Submitted: (Jan 07, 2021)
Evidence details

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 rs143443833...

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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