NM_032119.4(ADGRV1):c.6289C>T (p.Arg2097Cys) AND not specified

Clinical significance:Benign (Last evaluated: Dec 16, 2015)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000039606.9

Allele description [Variation Report for NM_032119.4(ADGRV1):c.6289C>T (p.Arg2097Cys)]

NM_032119.4(ADGRV1):c.6289C>T (p.Arg2097Cys)

Gene:
ADGRV1:adhesion G protein-coupled receptor V1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q14.3
Genomic location:
Preferred name:
NM_032119.4(ADGRV1):c.6289C>T (p.Arg2097Cys)
Other names:
p.R2097C:CGT>TGT
HGVS:
  • NC_000005.10:g.90685794C>T
  • NG_007083.2:g.161451C>T
  • NM_032119.4:c.6289C>TMANE SELECT
  • NP_115495.3:p.Arg2097Cys
  • LRG_1095t1:c.6289C>T
  • LRG_1095:g.161451C>T
  • LRG_1095p1:p.Arg2097Cys
  • NC_000005.9:g.89981611C>T
  • NM_032119.3:c.6289C>T
  • NR_003149.2:n.6388C>T
  • Q8WXG9:p.Arg2097Cys
  • c.6289C>T
Protein change:
R2097C
Links:
UniProtKB: Q8WXG9#VAR_046349; dbSNP: rs16868974
NCBI 1000 Genomes Browser:
rs16868974
Molecular consequence:
  • NM_032119.4:c.6289C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_003149.2:n.6388C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
100

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000063295Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Benign
(May 14, 2012)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000168706GeneDxcriteria provided, single submitter
Benign
(May 2, 2013)
germlineclinical testing

Citation Link,

SCV000193280Genetic Services Laboratory,University of Chicagono assertion criteria providedLikely benigngermlineclinical testing

SCV000338401EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Benign
(Dec 16, 2015)
germlineclinical testing

Citation Link

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed

SCV000193280

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot provided101100not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000063295.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided101not providednot providedclinical testing PubMed (1)

Description

Arg2097Cys in exon 29 of GPR98: This variant is not expected to have clinical si gnificance because it is has been identified in 1.3% (89/6626) of European Ameri can chromosomes and 10.0% (305/3030) of African American chromosomes from a broa d population by the NHLBI Exome sequencing project (http://evs.gs.washington.edu /EVS/; dbSNP rs16868974).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided101not provided100not provided

From GeneDx, SCV000168706.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genetic Services Laboratory,University of Chicago, SCV000193280.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000338401.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 27, 2021

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