chrX-153541366-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001001344.3(ATP2B3):c.216G>A(p.Ala72Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0019 in 1,210,503 control chromosomes in the GnomAD database, including 19 homozygotes. There are 844 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001001344.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00238 AC: 268AN: 112462Hom.: 3 Cov.: 24 AF XY: 0.00422 AC XY: 146AN XY: 34616
GnomAD3 exomes AF: 0.00328 AC: 601AN: 183030Hom.: 5 AF XY: 0.00319 AC XY: 216AN XY: 67652
GnomAD4 exome AF: 0.00185 AC: 2026AN: 1097990Hom.: 16 Cov.: 32 AF XY: 0.00192 AC XY: 698AN XY: 363476
GnomAD4 genome AF: 0.00238 AC: 268AN: 112513Hom.: 3 Cov.: 24 AF XY: 0.00421 AC XY: 146AN XY: 34677
ClinVar
Submissions by phenotype
not provided Benign:1
- -
ATP2B3-related disorder Benign:1
This variant is classified as 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