chrX-19344058-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_000284.4(PDHA1):c.21C>T(p.Ala7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000029 in 1,206,660 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A7A) has been classified 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 -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDHA1 | NM_000284.4 | c.21C>T | p.Ala7= | synonymous_variant | 1/11 | ENST00000422285.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDHA1 | ENST00000422285.7 | c.21C>T | p.Ala7= | synonymous_variant | 1/11 | 1 | NM_000284.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000178 AC: 2AN: 112631Hom.: 0 Cov.: 24 AF XY: 0.0000288 AC XY: 1AN XY: 34777
GnomAD3 exomes AF: 0.0000115 AC: 2AN: 173897Hom.: 0 AF XY: 0.0000160 AC XY: 1AN XY: 62657
GnomAD4 exome AF: 0.0000302 AC: 33AN: 1094029Hom.: 0 Cov.: 29 AF XY: 0.0000166 AC XY: 6AN XY: 361143
GnomAD4 genome ? AF: 0.0000178 AC: 2AN: 112631Hom.: 0 Cov.: 24 AF XY: 0.0000288 AC XY: 1AN XY: 34777
ClinVar
Submissions by phenotype
Pyruvate dehydrogenase E1-alpha deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at