chr11-112025600-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001931.5(DLAT):c.128C>T(p.Ala43Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 1,613,720 control chromosomes in the GnomAD database, including 108,574 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001931.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLAT | NM_001931.5 | c.128C>T | p.Ala43Val | missense_variant | 1/14 | ENST00000280346.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLAT | ENST00000280346.11 | c.128C>T | p.Ala43Val | missense_variant | 1/14 | 1 | NM_001931.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.334 AC: 50799AN: 152024Hom.: 9011 Cov.: 32
GnomAD3 exomes AF: 0.380 AC: 94757AN: 249216Hom.: 18833 AF XY: 0.380 AC XY: 51395AN XY: 135082
GnomAD4 exome AF: 0.366 AC: 534478AN: 1461578Hom.: 99562 Cov.: 80 AF XY: 0.367 AC XY: 267049AN XY: 727108
GnomAD4 genome AF: 0.334 AC: 50824AN: 152142Hom.: 9012 Cov.: 32 AF XY: 0.342 AC XY: 25423AN XY: 74356
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 15, 2016 | - - |
Pyruvate dehydrogenase E2 deficiency Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at