1-9553707-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_032315.3(SLC25A33):c.138C>T(p.Leu46Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000391 in 1,614,142 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_032315.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00208 AC: 317AN: 152144Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000505 AC: 127AN: 251484Hom.: 0 AF XY: 0.000316 AC XY: 43AN XY: 135914
GnomAD4 exome AF: 0.000215 AC: 314AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.000183 AC XY: 133AN XY: 727240
GnomAD4 genome AF: 0.00208 AC: 317AN: 152262Hom.: 2 Cov.: 32 AF XY: 0.00200 AC XY: 149AN XY: 74450
ClinVar
Submissions by phenotype
SLC25A33-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