NM_032119.4(ADGRV1):c.15471C>T (p.Ser5157=) AND not specified

Clinical significance:Benign/Likely benign (Last evaluated: May 19, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000039535.4

Allele description [Variation Report for NM_032119.4(ADGRV1):c.15471C>T (p.Ser5157=)]

NM_032119.4(ADGRV1):c.15471C>T (p.Ser5157=)

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.15471C>T (p.Ser5157=)
HGVS:
  • NC_000005.10:g.90810731C>T
  • NG_007083.2:g.286388C>T
  • NM_032119.4:c.15471C>TMANE SELECT
  • NP_115495.3:p.Ser5157=
  • LRG_1095t1:c.15471C>T
  • LRG_1095:g.286388C>T
  • LRG_1095p1:p.Ser5157=
  • NC_000005.9:g.90106548C>T
  • NM_032119.3:c.15471C>T
  • NR_003149.2:n.15487C>T
  • c.15471C>T
  • p.Ser5157Ser
Links:
dbSNP: rs146082509
NCBI 1000 Genomes Browser:
rs146082509
Molecular consequence:
  • NR_003149.2:n.15487C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_032119.4:c.15471C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
4

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
SCV000063224Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Likely benign
(Jun 20, 2017)
germlineclinical testing

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

SCV001880705Athena Diagnostics Inccriteria provided, single submitter
Benign
(May 19, 2021)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided44not providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot 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

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000063224.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided4not providednot providedclinical testing PubMed (1)

Description

p.Ser5157Ser in exon 74 of GPR98: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not predicte d to impact splicing. It has been identified in 0.2% (40/18870) of East Asian c hromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstit ute.org; dbSNP rs146082509).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided4not provided4not provided

From Athena Diagnostics Inc, SCV001880705.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2021

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