chr5-90558631-G-C

Position:

• chr5-90558631-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000508842.5(ADGRV1):​c.34+29116G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 620,114 control chromosomes in the GnomAD database, including 96,891 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.56 (23882 hom., cov: 31)
  • Exomes 𝑓: 0.55 (73009 hom.)
• Consequence: ADGRV1 ENST00000508842.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.404

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP6: Variant 5-90558631-G-C is Benign according to our data. Variant chr5-90558631-G-C is described in ClinVar as [Benign]. Clinvar id is 667600.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRV1	ENST00000508842.5	c.34+29116G>C		intron_variant		3		ENSP00000425936

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84811 AN: 151800 Hom.: 23853 Cov.: 31

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.546

GnomAD4 exome AF: 0.555 AC: 259712 AN: 468196 Hom.: 73009 AF XY: 0.562 AC XY: 140081 AN XY: 249474

Gnomad4 AFR exome AF: 0.605

Gnomad4 AMR exome AF: 0.416

Gnomad4 ASJ exome AF: 0.568

Gnomad4 EAS exome AF: 0.548

Gnomad4 SAS exome AF: 0.617

Gnomad4 FIN exome AF: 0.542

Gnomad4 NFE exome AF: 0.554

Gnomad4 OTH exome AF: 0.561

GnomAD4 genome AF: 0.559 AC: 84887 AN: 151918 Hom.: 23882 Cov.: 31 AF XY: 0.558 AC XY: 41443 AN XY: 74250

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.548

Alfa AF: 0.565 Hom.: 3030

Bravo AF: 0.550

Asia WGS AF: 0.592 AC: 2059 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	9.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs154568; hg19: chr5-89854448; COSMIC: COSV67991180;