chrX-153541734-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_001001344.3(ATP2B3):c.472G>T(p.Ala158Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000364 in 1,209,974 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A158V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001001344.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2B3 | NM_001001344.3 | c.472G>T | p.Ala158Ser | missense_variant | 5/22 | ENST00000263519.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2B3 | ENST00000263519.5 | c.472G>T | p.Ala158Ser | missense_variant | 5/22 | 1 | NM_001001344.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000625 AC: 7AN: 111968Hom.: 0 Cov.: 23 AF XY: 0.0000586 AC XY: 2AN XY: 34138
GnomAD3 exomes AF: 0.0000928 AC: 17AN: 183201Hom.: 0 AF XY: 0.0000591 AC XY: 4AN XY: 67709
GnomAD4 exome AF: 0.0000337 AC: 37AN: 1097952Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 11AN XY: 363458
GnomAD4 genome ? AF: 0.0000625 AC: 7AN: 112022Hom.: 0 Cov.: 23 AF XY: 0.0000585 AC XY: 2AN XY: 34202
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2021 | The c.472G>T (p.A158S) alteration is located in exon 3 (coding exon 3) of the ATP2B3 gene. This alteration results from a G to T substitution at nucleotide position 472, causing the alanine (A) at amino acid position 158 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
X-linked progressive cerebellar ataxia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at