chr5-90558495-C-G

Variant names:

• chr5-90558495-C-G
• rs154570
• ENST00000508842.5:c.34+28980C>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRV1	ENST00000508842.5	c.34+28980C>G		intron_variant	Intron 1 of 3	3		ENSP00000425936.1

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;