chr2-218425738-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_007127.3(VIL1):c.274C>T(p.Arg92Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000496 in 1,614,140 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R92Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_007127.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VIL1 | NM_007127.3 | c.274C>T | p.Arg92Trp | missense_variant | 4/20 | ENST00000248444.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VIL1 | ENST00000248444.10 | c.274C>T | p.Arg92Trp | missense_variant | 4/20 | 1 | NM_007127.3 | P1 | |
VIL1 | ENST00000440053.1 | c.274C>T | p.Arg92Trp | missense_variant | 3/9 | 1 | |||
VIL1 | ENST00000454069.5 | c.274C>T | p.Arg92Trp | missense_variant | 4/6 | 3 | |||
VIL1 | ENST00000392114.6 | c.-183-3730C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000256 AC: 39AN: 152176Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00102 AC: 256AN: 251242Hom.: 5 AF XY: 0.00152 AC XY: 207AN XY: 135804
GnomAD4 exome AF: 0.000521 AC: 761AN: 1461846Hom.: 10 Cov.: 31 AF XY: 0.000802 AC XY: 583AN XY: 727224
GnomAD4 genome ? AF: 0.000256 AC: 39AN: 152294Hom.: 1 Cov.: 33 AF XY: 0.000443 AC XY: 33AN XY: 74454
ClinVar
Submissions by phenotype
VIL1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 11, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at