rs374609813
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_032119.4(ADGRV1):āc.2261T>Cā(p.Val754Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000868 in 1,613,274 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032119.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.2261T>C | p.Val754Ala | missense_variant | Exon 12 of 90 | 1 | NM_032119.4 | ENSP00000384582.2 | ||
ADGRV1 | ENST00000640403 | c.-437T>C | 5_prime_UTR_variant | Exon 2 of 29 | 5 | ENSP00000492531.1 | ||||
ADGRV1 | ENST00000504142.2 | n.1027T>C | non_coding_transcript_exon_variant | Exon 6 of 14 | 5 | |||||
ADGRV1 | ENST00000639676.1 | n.-235T>C | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152158Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000141 AC: 35AN: 248760Hom.: 2 AF XY: 0.000207 AC XY: 28AN XY: 134966
GnomAD4 exome AF: 0.0000890 AC: 130AN: 1461116Hom.: 3 Cov.: 32 AF XY: 0.000125 AC XY: 91AN XY: 726816
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152158Hom.: 1 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The Val754Ala variant in GPR98 has not been previously reported in individuals w ith hearing loss, but has been identified in 0.03% (2/8154) of European American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu /EVS/; dbSNP rs374609813). Although this variant has been seen in the general po pulation, its frequency is not high enough to rule out a pathogenic role. Compu tational prediction tools and conservation analyses do not provide strong suppor t for or against an impact to the protein. In summary, the clinical significance of the Val754Ala variant is uncertain. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at