rs767503319
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_000284.4(PDHA1):c.984T>C(p.Asn328=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000833 in 1,177,023 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 28 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000284.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDHA1 | NM_000284.4 | c.984T>C | p.Asn328= | synonymous_variant | 10/11 | ENST00000422285.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDHA1 | ENST00000422285.7 | c.984T>C | p.Asn328= | synonymous_variant | 10/11 | 1 | NM_000284.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000896 AC: 10AN: 111586Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33750
GnomAD3 exomes AF: 0.0000327 AC: 6AN: 183318Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67772
GnomAD4 exome AF: 0.0000826 AC: 88AN: 1065437Hom.: 0 Cov.: 26 AF XY: 0.0000838 AC XY: 28AN XY: 334097
GnomAD4 genome ? AF: 0.0000896 AC: 10AN: 111586Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33750
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 23, 2014 | - - |
Pyruvate dehydrogenase E1-alpha deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2017 | 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. - |
Pyruvate dehydrogenase complex deficiency Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at