5-90701231-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032119.4(ADGRV1):c.8156-2434A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 152,160 control chromosomes in the GnomAD database, including 367 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.060 (367 hom., cov: 32)
• Consequence: ADGRV1 NM_032119.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADGRV1	NM_032119.4	c.8156-2434A>T		intron_variant		ENST00000405460.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADGRV1	ENST00000405460.9	c.8156-2434A>T		intron_variant		1	NM_032119.4	P1

Frequencies

GnomAD3 genomes AF: 0.0602 AC: 9147 AN: 152042 Hom.: 369 Cov.: 32

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0600

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0808

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0601 AC: 9140 AN: 152160 Hom.: 367 Cov.: 32 AF XY: 0.0601 AC XY: 4475 AN XY: 74400

Gnomad4 AFR AF: 0.0254

Gnomad4 AMR AF: 0.0599

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.00541

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0485

Gnomad4 NFE AF: 0.0808

Gnomad4 OTH AF: 0.0655

Alfa AF: 0.0684 Hom.: 45

Bravo AF: 0.0562

Asia WGS AF: 0.0550 AC: 189 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.3
Dann	Benign	0.71

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: rs10514332; hg19: chr5-89997048;