chr11-792955-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6BP7BS1
The NM_001191061.2(SLC25A22):c.327G>A(p.Ala109Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000485 in 1,613,440 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A109A) has been classified as Likely benign.
Frequency
Consequence
NM_001191061.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000506 AC: 77AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000372 AC: 93AN: 249888Hom.: 0 AF XY: 0.000317 AC XY: 43AN XY: 135582
GnomAD4 exome AF: 0.000483 AC: 706AN: 1461176Hom.: 1 Cov.: 38 AF XY: 0.000483 AC XY: 351AN XY: 726918
GnomAD4 genome AF: 0.000506 AC: 77AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74444
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
- -
SLC25A22: BP4, BP7 -
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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. -
Early infantile epileptic encephalopathy with suppression bursts Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at