chr5-90558495-C-G

Position:

• chr5-90558495-C-G

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+28980C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,008 control chromosomes in the GnomAD database, including 27,642 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.60 (27642 hom., cov: 32)
• Consequence: ADGRV1 ENST00000508842.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.15

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=-0.74).
• BP6: Variant 5-90558495-C-G is Benign according to our data. Variant chr5-90558495-C-G is described in ClinVar as [Benign]. Clinvar id is 1249930.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 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+28980C>G		intron_variant		3		ENSP00000425936

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90535 AN: 151890 Hom.: 27605 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.572

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.596 AC: 90621 AN: 152008 Hom.: 27642 Cov.: 32 AF XY: 0.594 AC XY: 44170 AN XY: 74306

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.464

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: 0.574

Alfa AF: 0.585 Hom.: 3286

Bravo AF: 0.592

Asia WGS AF: 0.600 AC: 2086 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

Jul 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.066
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: rs154570; hg19: chr5-89854312;