rs61757217
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001931.5(DLAT):c.55G>C(p.Glu19Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00827 in 1,614,048 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00686 AC: 1045AN: 152246Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00735 AC: 1835AN: 249764Hom.: 13 AF XY: 0.00741 AC XY: 1003AN XY: 135294
GnomAD4 exome AF: 0.00842 AC: 12311AN: 1461684Hom.: 65 Cov.: 30 AF XY: 0.00831 AC XY: 6042AN XY: 727170
GnomAD4 genome AF: 0.00686 AC: 1045AN: 152364Hom.: 5 Cov.: 33 AF XY: 0.00651 AC XY: 485AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:5
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DLAT: BP4, BS2 -
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Pyruvate dehydrogenase E2 deficiency Benign:3
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not specified Benign:1
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. -
DLAT-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at