dbSNP rs71614763: ADGRV1:c.8730+21dupT (chr5-90706403-C-CT) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_032119.4(ADGRV1):c.8730+21dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 35884 hom., cov: 0)

Exomes 𝑓: 0.45 ( 13569 hom. )

Failed GnomAD Quality Control

Consequence

ADGRV1
NM_032119.4 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.0450

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 5-90706403-C-CT is Benign according to our data. Variant chr5-90706403-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 197047.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRV1	NM_032119.4 link	c.8730+21dupT		intron_variant	Intron 38 of 89	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.8730+9_8730+10insT		intron_variant	Intron 38 of 89	1	NM_032119.4	ENSP00000384582.2		Q8WXG9-1

Frequencies

GnomAD3 genomes

AF:

0.700

AC:

102421

AN:

146356

Hom.:

35860

Cov.:

show subpopulations

Gnomad AFR

AF:

0.806

Gnomad AMI

AF:

0.673

Gnomad AMR

AF:

0.714

Gnomad ASJ

AF:

0.663

Gnomad EAS

AF:

0.791

Gnomad SAS

AF:

0.728

Gnomad FIN

AF:

0.626

Gnomad MID

AF:

0.677

Gnomad NFE

AF:

0.636

Gnomad OTH

AF:

0.708

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.450

AC:

545934

AN:

1213242

Hom.:

13569

Cov.:

AF XY:

0.449

AC XY:

269704

AN XY:

600146

show subpopulations

Gnomad4 AFR exome

AF:

0.495

Gnomad4 AMR exome

AF:

0.448

Gnomad4 ASJ exome

AF:

0.449

Gnomad4 EAS exome

AF:

0.482

Gnomad4 SAS exome

AF:

0.461

Gnomad4 FIN exome

AF:

0.444

Gnomad4 NFE exome

AF:

0.447

Gnomad4 OTH exome

AF:

0.458

GnomAD4 genome

AF:

0.700

AC:

102477

AN:

146434

Hom.:

35884

Cov.:

AF XY:

0.700

AC XY:

49842

AN XY:

71218

show subpopulations

Gnomad4 AFR

AF:

0.806

Gnomad4 AMR

AF:

0.714

Gnomad4 ASJ

AF:

0.663

Gnomad4 EAS

AF:

0.792

Gnomad4 SAS

AF:

0.726

Gnomad4 FIN

AF:

0.626

Gnomad4 NFE

AF:

0.636

Gnomad4 OTH

AF:

0.711

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Aug 21, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not specified

Benign:2

Dec 19, 2014

Eurofins Ntd Llc (ga)

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Usher syndrome type 2C

Benign:1

Nov 20, 2020

Molecular Genetics, Royal Melbourne Hospital

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Population allele frequency is 3% (rs60522638, 4,300/138,988 alleles, 1 homozygote in gnomAD v2.1). Based on the classification scheme RMH ACMG Guidelines v1.1.1, this variant is classified as Benign. Following criteria met: BA1 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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