5-90805341-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032119.4(ADGRV1):c.14719G>T(p.Val4907Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000465 in 1,612,314 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_032119.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 248956Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135034
GnomAD4 exome AF: 0.0000473 AC: 69AN: 1460138Hom.: 0 Cov.: 30 AF XY: 0.0000413 AC XY: 30AN XY: 726318
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The p.Val4907Phe variant in ADGRV1 has not been previously reported in individuals with hearing loss or Usher syndrome, but it has been identified in 0.007% (8/112882) European chromosomes by gnomAD (http://gnomad.broadinstitute.org). It has been reported in ClinVar (Variation ID 504584). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. Computational prediction tools and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. In summary, the clinical significance of the p.Val4907Phe variant is uncertain. ACMG/AMP Criteria applied: PM2, BP4. -
Febrile seizures, familial, 4;C2931213:Usher syndrome type 2C Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at