chr2-218423794-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_007127.3(VIL1):c.16G>A(p.Ala6Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000466 in 1,614,118 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_007127.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VIL1 | NM_007127.3 | c.16G>A | p.Ala6Thr | missense_variant | 2/20 | ENST00000248444.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VIL1 | ENST00000248444.10 | c.16G>A | p.Ala6Thr | missense_variant | 2/20 | 1 | NM_007127.3 | P1 | |
VIL1 | ENST00000440053.1 | c.16G>A | p.Ala6Thr | missense_variant | 1/9 | 1 | |||
VIL1 | ENST00000454069.5 | c.16G>A | p.Ala6Thr | missense_variant | 2/6 | 3 | |||
VIL1 | ENST00000392114.6 | c.-184+4626G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00208 AC: 317AN: 152156Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000640 AC: 161AN: 251386Hom.: 0 AF XY: 0.000427 AC XY: 58AN XY: 135880
GnomAD4 exome AF: 0.000298 AC: 435AN: 1461844Hom.: 2 Cov.: 32 AF XY: 0.000252 AC XY: 183AN XY: 727230
GnomAD4 genome ? AF: 0.00208 AC: 317AN: 152274Hom.: 1 Cov.: 32 AF XY: 0.00197 AC XY: 147AN XY: 74436
ClinVar
Submissions by phenotype
VIL1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 12, 2019 | This variant is classified as likely 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