rs376401006
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_032119.4(ADGRV1):āc.4487A>Gā(p.Tyr1496Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0001 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. Y1496Y) has been classified as Likely benign.
Frequency
Consequence
NM_032119.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRV1 | NM_032119.4 | c.4487A>G | p.Tyr1496Cys | missense_variant | 21/90 | ENST00000405460.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.4487A>G | p.Tyr1496Cys | missense_variant | 21/90 | 1 | NM_032119.4 | P1 | |
ADGRV1 | ENST00000640403.1 | c.1778A>G | p.Tyr593Cys | missense_variant | 11/29 | 5 | |||
ADGRV1 | ENST00000639676.1 | n.2085A>G | non_coding_transcript_exon_variant | 9/11 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000512 AC: 78AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 30AN: 249216Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135200
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461670Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 727114
GnomAD4 genome AF: 0.000525 AC: 80AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74488
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 12, 2016 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.4487A>G (p.Y1496C) alteration is located in exon 21 (coding exon 21) of the ADGRV1 gene. This alteration results from a A to G substitution at nucleotide position 4487, causing the tyrosine (Y) at amino acid position 1496 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Febrile seizures, familial, 4;C2931213:Usher syndrome type 2C Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at