3-193412265-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_032279.4(ATP13A4):c.3121G>A(p.Val1041Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,613,472 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_032279.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000657 AC: 100AN: 152162Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000147 AC: 37AN: 251470Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135910
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461192Hom.: 0 Cov.: 31 AF XY: 0.0000536 AC XY: 39AN XY: 726950
GnomAD4 genome AF: 0.000657 AC: 100AN: 152280Hom.: 1 Cov.: 32 AF XY: 0.000672 AC XY: 50AN XY: 74458
ClinVar
Submissions by phenotype
not specified 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. -
ATP13A4-related disorder Benign:1
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). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at