chr5-91153337-G-A

Variant names:

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_032119.4(ADGRV1):c.18741G>A(p.Gly6247Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,611,782 control chromosomes in the GnomAD database, including 11,031 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1164 hom., cov: 32)

Exomes 𝑓: 0.11 ( 9867 hom. )

Consequence

ADGRV1
NM_032119.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.621

Variant links:

Genes affected

ADGRV1 (HGNC:17416): (adhesion G protein-coupled receptor V1) This gene encodes a member of the G-protein coupled receptor superfamily. The encoded protein contains a 7-transmembrane receptor domain, binds calcium and is expressed in the central nervous system. Mutations in this gene are associated with Usher syndrome 2 and familial febrile seizures. Several alternatively spliced transcripts have been described. [provided by RefSeq, Jul 2008]

ADGRV1 links:

LUCAT1 (HGNC:48498): (lung cancer associated transcript 1)

LUCAT1 links:

LOC107986432 (HGNC:):

LOC107986432 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP6

Variant 5-91153337-G-A is Benign according to our data. Variant chr5-91153337-G-A is described in ClinVar as [Benign]. Clinvar id is 46300.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-91153337-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.621 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRV1	NM_032119.4 link	c.18741G>A	p.Gly6247Gly	synonymous_variant	Exon 89 of 90	ENST00000405460.9	NP_115495.3	Q8WXG9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRV1	ENST00000405460.9 link	c.18741G>A	p.Gly6247Gly	synonymous_variant	Exon 89 of 90	1	NM_032119.4	ENSP00000384582.2		Q8WXG9-1

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18211

AN:

152048

Hom.:

1164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.123

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.169

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.119

GnomAD3 exomes

AF:

0.117

AC:

28963

AN:

246562

Hom.:

1778

AF XY:

0.121

AC XY:

16122

AN XY:

133750

show subpopulations

Gnomad AFR exome

AF:

0.137

Gnomad AMR exome

AF:

0.0877

Gnomad ASJ exome

AF:

0.119

Gnomad EAS exome

AF:

0.123

Gnomad SAS exome

AF:

0.175

Gnomad FIN exome

AF:

0.108

Gnomad NFE exome

AF:

0.109

Gnomad OTH exome

AF:

0.110

GnomAD4 exome

AF:

0.112

AC:

163913

AN:

1459616

Hom.:

9867

Cov.:

AF XY:

0.115

AC XY:

83304

AN XY:

725954

show subpopulations

Gnomad4 AFR exome

AF:

0.142

Gnomad4 AMR exome

AF:

0.0882

Gnomad4 ASJ exome

AF:

0.121

Gnomad4 EAS exome

AF:

0.167

Gnomad4 SAS exome

AF:

0.176

Gnomad4 FIN exome

AF:

0.103

Gnomad4 NFE exome

AF:

0.105

Gnomad4 OTH exome

AF:

0.114

GnomAD4 genome

AF:

0.120

AC:

18233

AN:

152166

Hom.:

1164

Cov.:

AF XY:

0.123

AC XY:

9168

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.139

Gnomad4 AMR

AF:

0.106

Gnomad4 ASJ

AF:

0.123

Gnomad4 EAS

AF:

0.132

Gnomad4 SAS

AF:

0.191

Gnomad4 FIN

AF:

0.109

Gnomad4 NFE

AF:

0.107

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.108

Hom.:

1906

Bravo

AF:

0.117

Asia WGS

AF:

0.136

AC:

474

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Feb 26, 2016

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 19, 2009

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 07, 2013

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Usher syndrome type 2C

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Febrile seizures, familial, 4;C2931213:Usher syndrome type 2C

Benign:1

Sep 08, 2021

Fulgent Genetics, Fulgent Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

1.9

DANN

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over