X-19344067-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000284.4(PDHA1):c.30C>T(p.Arg10Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000914 in 1,093,884 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000284.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDHA1 | NM_000284.4 | c.30C>T | p.Arg10Arg | synonymous_variant | Exon 1 of 11 | ENST00000422285.7 | NP_000275.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 exomes AF: 0.00000577 AC: 1AN: 173334Hom.: 0 AF XY: 0.0000161 AC XY: 1AN XY: 62234
GnomAD4 exome AF: 9.14e-7 AC: 1AN: 1093884Hom.: 0 Cov.: 29 AF XY: 0.00000277 AC XY: 1AN XY: 361020
GnomAD4 genome Cov.: 25
ClinVar
Submissions by phenotype
Pyruvate dehydrogenase E1-alpha deficiency Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at