rs35899901
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_003850.3(SUCLA2):c.45C>T(p.Thr15Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,608,188 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003850.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00572 AC: 870AN: 152180Hom.: 5 Cov.: 34
GnomAD3 exomes AF: 0.00150 AC: 353AN: 235038Hom.: 3 AF XY: 0.00106 AC XY: 136AN XY: 128320
GnomAD4 exome AF: 0.000515 AC: 750AN: 1455890Hom.: 6 Cov.: 34 AF XY: 0.000417 AC XY: 302AN XY: 723902
GnomAD4 genome AF: 0.00573 AC: 873AN: 152298Hom.: 5 Cov.: 34 AF XY: 0.00539 AC XY: 401AN XY: 74466
ClinVar
Submissions by phenotype
not specified Benign:3
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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. -
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not provided Benign:2
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Mitochondrial DNA depletion syndrome, encephalomyopathic form with methylmalonic aciduria Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at