rs370906851
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032119.4(ADGRV1):c.16331C>A(p.Thr5444Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000529 in 1,613,808 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T5444A) has been classified as Uncertain significance.
Frequency
Consequence
NM_032119.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRV1 | NM_032119.4 | c.16331C>A | p.Thr5444Lys | missense_variant | 76/90 | ENST00000405460.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRV1 | ENST00000405460.9 | c.16331C>A | p.Thr5444Lys | missense_variant | 76/90 | 1 | NM_032119.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000368 AC: 56AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000337 AC: 84AN: 249132Hom.: 0 AF XY: 0.000281 AC XY: 38AN XY: 135158
GnomAD4 exome AF: 0.000545 AC: 797AN: 1461536Hom.: 0 Cov.: 33 AF XY: 0.000536 AC XY: 390AN XY: 727040
GnomAD4 genome ? AF: 0.000368 AC: 56AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.000389 AC XY: 29AN XY: 74456
ClinVar
Submissions by phenotype
not provided Uncertain:3Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 03, 2015 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 29, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2019 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 28, 2022 | Variant summary: ADGRV1 c.16331C>A (p.Thr5444Lys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00034 in 249132 control chromosomes (gnomAD). This frequency is not higher than predicted for a pathogenic variant in ADGRV1 causing Usher Syndrome (0.00034 vs 0.0054), allowing no conclusion about variant significance. c.16331C>A has been reported in the literature in individuals affected with Usher Syndrome/deafness with non-informative genotypes (pathogenicity of the second allele uncertain) (examples: Sloan-Heggen_2016 and Zhou_2022). These report(s) do not provide unequivocal conclusions about association of the variant with Usher Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
ADGRV1-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 04, 2023 | The ADGRV1 c.16331C>A variant is predicted to result in the amino acid substitution p.Thr5444Lys. This variant was reported in the heterozygous state along with a second potentially causative variant (p.Ile508Leu) in an individual with hearing loss (Table S3, Sloan-Heggen. 2016. PubMed ID: 26969326). This variant is reported in 0.065% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
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