Variant 5-90642617-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032119.4(ADGRV1):c.2241-19G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,604,350 control chromosomes in the GnomAD database, including 24,003 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2691 hom., cov: 32)

Exomes 𝑓: 0.16 ( 21312 hom. )

Consequence

ADGRV1
NM_032119.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.615

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 5-90642617-G-T is Benign according to our data. Variant chr5-90642617-G-T is described in ClinVar as [Benign]. Clinvar id is 137502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-90642617-G-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADGRV1	NM_032119.4 linkuse as main transcript	c.2241-19G>T		intron_variant		ENST00000405460.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
ADGRV1	ENST00000405460.9 linkuse as main transcript	c.2241-19G>T	intron_variant	1	NM_032119.4	P1	Q8WXG9-1
ADGRV1	ENST00000640403.1 linkuse as main transcript	c.-457-19G>T	intron_variant	5
ADGRV1	ENST00000504142.2 linkuse as main transcript	n.1007-19G>T	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27498

AN:

151870

Hom.:

2679

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.120

Gnomad AMR

AF:

0.150

Gnomad ASJ

AF:

0.221

Gnomad EAS

AF:

0.402

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.175

GnomAD3 exomes

AF:

0.188

AC:

45269

AN:

240940

Hom.:

4885

AF XY:

0.188

AC XY:

24485

AN XY:

130442

show subpopulations

Gnomad AFR exome

AF:

0.201

Gnomad AMR exome

AF:

0.141

Gnomad ASJ exome

AF:

0.222

Gnomad EAS exome

AF:

0.404

Gnomad SAS exome

AF:

0.225

Gnomad FIN exome

AF:

0.191

Gnomad NFE exome

AF:

0.153

Gnomad OTH exome

AF:

0.175

GnomAD4 exome

AF:

0.164

AC:

237845

AN:

1452362

Hom.:

21312

Cov.:

AF XY:

0.166

AC XY:

119757

AN XY:

721968

show subpopulations

Gnomad4 AFR exome

AF:

0.204

Gnomad4 AMR exome

AF:

0.142

Gnomad4 ASJ exome

AF:

0.218

Gnomad4 EAS exome

AF:

0.385

Gnomad4 SAS exome

AF:

0.225

Gnomad4 FIN exome

AF:

0.184

Gnomad4 NFE exome

AF:

0.148

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

AF:

0.181

AC:

27539

AN:

151988

Hom.:

2691

Cov.:

AF XY:

0.185

AC XY:

13751

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.201

Gnomad4 AMR

AF:

0.150

Gnomad4 ASJ

AF:

0.221

Gnomad4 EAS

AF:

0.403

Gnomad4 SAS

AF:

0.230

Gnomad4 FIN

AF:

0.183

Gnomad4 NFE

AF:

0.154

Gnomad4 OTH

AF:

0.182

Alfa

AF:

0.157

Hom.:

2703

Bravo

AF:

0.179

Asia WGS

AF:

0.316

AC:

1097

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 08, 2013	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. -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Usher syndrome type 2C

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.6

DANN

Benign

0.50

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