chr13-113652931-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000705.4(ATP4B):c.497C>T(p.Ala166Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00158 in 1,614,158 control chromosomes in the GnomAD database, including 29 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A166E) has been classified as Uncertain significance.
Frequency
Consequence
NM_000705.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP4B | NM_000705.4 | c.497C>T | p.Ala166Val | missense_variant | 4/7 | ENST00000335288.5 | |
GRK1 | XM_047430493.1 | c.-7+4687G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP4B | ENST00000335288.5 | c.497C>T | p.Ala166Val | missense_variant | 4/7 | 1 | NM_000705.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00795 AC: 1210AN: 152156Hom.: 16 Cov.: 33
GnomAD3 exomes AF: 0.00236 AC: 593AN: 251454Hom.: 5 AF XY: 0.00163 AC XY: 221AN XY: 135900
GnomAD4 exome AF: 0.000912 AC: 1333AN: 1461884Hom.: 13 Cov.: 31 AF XY: 0.000815 AC XY: 593AN XY: 727240
GnomAD4 genome ? AF: 0.00797 AC: 1214AN: 152274Hom.: 16 Cov.: 33 AF XY: 0.00772 AC XY: 575AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2024 | 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