2-218427969-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007127.3(VIL1):c.352C>T(p.Arg118Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,613,766 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 Uncertain significance (★).
Frequency
Consequence
NM_007127.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VIL1 | ENST00000248444.10 | c.352C>T | p.Arg118Trp | missense_variant | Exon 5 of 20 | 1 | NM_007127.3 | ENSP00000248444.5 | ||
VIL1 | ENST00000440053.1 | c.352C>T | p.Arg118Trp | missense_variant | Exon 4 of 9 | 1 | ENSP00000409270.1 | |||
VIL1 | ENST00000454069.5 | c.340C>T | p.Arg114Trp | missense_variant | Exon 5 of 6 | 3 | ENSP00000412657.1 | |||
VIL1 | ENST00000392114.6 | c.-183-1499C>T | intron_variant | Intron 1 of 14 | 2 | ENSP00000375962.2 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251226Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135764
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461632Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727128
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.352C>T (p.R118W) alteration is located in exon 5 (coding exon 4) of the VIL1 gene. This alteration results from a C to T substitution at nucleotide position 352, causing the arginine (R) at amino acid position 118 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at