chr5-90704137-T-C

Position:

• chr5-90704137-T-C

Variant summary

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

The NM_032119.4(ADGRV1):​c.8287-252T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 151,694 control chromosomes in the GnomAD database, including 33,496 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.66 (33496 hom., cov: 32)
• Consequence: ADGRV1 NM_032119.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.123

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=-0.9).
• BP6: Variant 5-90704137-T-C is Benign according to our data. Variant chr5-90704137-T-C is described in ClinVar as [Benign]. Clinvar id is 1228117.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRV1	NM_032119.4	c.8287-252T>C		intron_variant		ENST00000405460.9	NP_115495.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRV1	ENST00000405460.9	c.8287-252T>C		intron_variant		1	NM_032119.4	ENSP00000384582.2

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99265 AN: 151576 Hom.: 33429 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.655 AC: 99393 AN: 151694 Hom.: 33496 Cov.: 32 AF XY: 0.658 AC XY: 48773 AN XY: 74116

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.674

Alfa AF: 0.594 Hom.: 26974

Bravo AF: 0.678

Asia WGS AF: 0.745 AC: 2589 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	-0.90
CADD	Benign	2.0
DANN	Benign	0.48

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

Other links and lift over

dbSNP: rs10942605; hg19: chr5-89999954;