7-38726968-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_014396.4(VPS41):c.2425G>A(p.Val809Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000017 in 1,584,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014396.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS41 | NM_014396.4 | c.2425G>A | p.Val809Met | missense_variant | Exon 28 of 29 | ENST00000310301.9 | NP_055211.2 | |
VPS41 | NM_080631.4 | c.2350G>A | p.Val784Met | missense_variant | Exon 27 of 28 | NP_542198.2 | ||
VPS41 | XM_017011988.2 | c.1270G>A | p.Val424Met | missense_variant | Exon 15 of 16 | XP_016867477.1 | ||
VPS41 | XR_007060008.1 | n.2536G>A | non_coding_transcript_exon_variant | Exon 29 of 29 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000219 AC: 5AN: 228410Hom.: 0 AF XY: 0.0000322 AC XY: 4AN XY: 124190
GnomAD4 exome AF: 0.0000181 AC: 26AN: 1432846Hom.: 0 Cov.: 30 AF XY: 0.0000168 AC XY: 12AN XY: 712644
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at