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NM_032119.4(ADGRV1):c.12269C>A (p.Thr4090Asn)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(4);Pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 30, 2021)
Last evaluated:
Nov 22, 2020
Accession:
VCV000046259.14
Variation ID:
46259
Description:
single nucleotide variant
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NM_032119.4(ADGRV1):c.12269C>A (p.Thr4090Asn)

Allele ID
55424
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q14.3
Genomic location
5: 90763453 (GRCh38) GRCh38 UCSC
5: 90059270 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.9:g.90059270C>A
LRG_1095:g.239110C>A
LRG_1095t1:c.12269C>A LRG_1095p1:p.Thr4090Asn
... more HGVS
Protein change
T4090N
Other names
p.T4090N:ACC>AAC
Canonical SPDI
NC_000005.10:90763452:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00246
The Genome Aggregation Database (gnomAD), exomes 0.00287
Trans-Omics for Precision Medicine (TOPMed) 0.00320
Trans-Omics for Precision Medicine (TOPMed) 0.00362
The Genome Aggregation Database (gnomAD) 0.00287
The Genome Aggregation Database (gnomAD) 0.00372
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00428
Links
ClinGen: CA138009
dbSNP: rs199839743
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 Feb 20, 2015 RCV000039515.5
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001155716.1
Conflicting interpretations of pathogenicity 5 criteria provided, conflicting interpretations Nov 22, 2020 RCV000419837.9
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ADGRV1 - - GRCh38
GRCh37
2423 2454

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jul 05, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000840641.1
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (1)
Likely benign
(Nov 22, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001101059.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jan 16, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000168721.11
Submitted: (Sep 30, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 26969326, 30180840, 32707200)
Likely Benign
(Dec 15, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000510804.1
Submitted: (Feb 17, 2017)
Evidence details
Comment:
Converted during submission to Likely benign.
Likely benign
(Feb 20, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000231442.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Apr 30, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000063204.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Thr4090Asn in Exon 59 of GPR98: This variant is not expected to have clinical si gnificance because it has been identified in 0.6% (39/6606) of … (more)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2C
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001317171.1
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)
Pathogenic
(Jul 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001154446.7
Submitted: (Jul 04, 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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Title Author Journal Year Link
Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss. Sloan-Heggen CM Human genetics 2016 PMID: 26969326
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ADGRV1 - - - -

Text-mined citations for rs199839743...

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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 27, 2021