chr5-90740272-A-G

Position:

• chr5-90740272-A-G

Variant summary

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

The ENST00000405460.9(ADGRV1):​c.10550-4774A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 151,868 control chromosomes in the GnomAD database, including 39,746 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 0.72 (39746 hom., cov: 29)
• Consequence: ADGRV1 ENST00000405460.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

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]

LOC105379077 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRV1	NM_032119.4	c.10550-4774A>G		intron_variant		ENST00000405460.9	NP_115495.3
LOC105379077	XR_001742802.2	n.363+635T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRV1	ENST00000405460.9	c.10550-4774A>G		intron_variant		1	NM_032119.4	ENSP00000384582	P1

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109066 AN: 151748 Hom.: 39677 Cov.: 29

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.719 AC: 109203 AN: 151868 Hom.: 39746 Cov.: 29 AF XY: 0.725 AC XY: 53865 AN XY: 74246

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.723

Alfa AF: 0.665 Hom.: 69102

Bravo AF: 0.729

Asia WGS AF: 0.791 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.52
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2222244; hg19: chr5-90036089;