NM_032119.4(ADGRV1):c.12269C>A (p.Thr4090Asn) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Likely benign(3);Pathogenic(1) (Last evaluated: Nov 22, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
5 submissions [Details]
Record status:
current
Accession:
RCV000419837.9

Allele description [Variation Report for NM_032119.4(ADGRV1):c.12269C>A (p.Thr4090Asn)]

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

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.12269C>A (p.Thr4090Asn)
Other names:
p.T4090N:ACC>AAC
HGVS:
  • NC_000005.10:g.90763453C>A
  • NG_007083.2:g.239110C>A
  • NM_032119.4:c.12269C>AMANE SELECT
  • NP_115495.3:p.Thr4090Asn
  • LRG_1095t1:c.12269C>A
  • LRG_1095:g.239110C>A
  • LRG_1095p1:p.Thr4090Asn
  • NC_000005.9:g.90059270C>A
  • NM_032119.3:c.12269C>A
  • NR_003149.2:n.12285C>A
  • c.12269C>A
Protein change:
T4090N
Links:
dbSNP: rs199839743
NCBI 1000 Genomes Browser:
rs199839743
Molecular consequence:
  • NM_032119.4:c.12269C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_003149.2:n.12285C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
2

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000168721GeneDxcriteria provided, single submitter
Benign
(Jan 16, 2019)
germlineclinical testing

Citation Link,

SCV000510804Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinicscriteria provided, single submitter
Likely Benign
(Dec 15, 2016)
germlineclinical testing

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

SCV000840641Athena Diagnostics Inccriteria provided, single submitter
Likely benign
(Jul 5, 2018)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001101059Invitaecriteria provided, single submitter
Likely benign
(Nov 22, 2020)
germlineclinical testing

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

SCV001154446CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Pathogenic
(Jul 1, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss.

Sloan-Heggen CM, Bierer AO, Shearer AE, Kolbe DL, Nishimura CJ, Frees KL, Ephraim SS, Shibata SB, Booth KT, Campbell CA, Ranum PT, Weaver AE, Black-Ziegelbein EA, Wang D, Azaiez H, Smith RJH.

Hum Genet. 2016 Apr;135(4):441-450. doi: 10.1007/s00439-016-1648-8. Epub 2016 Mar 11.

PubMed [citation]
PMID:
26969326
PMCID:
PMC4796320
See all PubMed Citations (4)

Details of each submission

From GeneDx, SCV000168721.11

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

Description

This variant is associated with the following publications: (PMID: 26969326, 30180840, 32707200)

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

From Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics, SCV000510804.1

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

Description

Converted during submission to Likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot provided0.005566not providednot provided

From Athena Diagnostics Inc, SCV000840641.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001101059.3

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

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001154446.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

Last Updated: Nov 27, 2021

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