6-24503366-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 4P and 5B. PM1PM2BP4_StrongBP6
The NM_001080.3(ALDH5A1):c.542C>T(p.Thr181Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000545 in 1,614,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T181A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001080.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH5A1 | NM_001080.3 | c.542C>T | p.Thr181Ile | missense_variant | 3/10 | ENST00000357578.8 | |
ALDH5A1 | NM_170740.1 | c.542C>T | p.Thr181Ile | missense_variant | 3/11 | ||
ALDH5A1 | NM_001368954.1 | c.542C>T | p.Thr181Ile | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH5A1 | ENST00000357578.8 | c.542C>T | p.Thr181Ile | missense_variant | 3/10 | 1 | NM_001080.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000916 AC: 23AN: 251214Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135786
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461742Hom.: 0 Cov.: 33 AF XY: 0.0000303 AC XY: 22AN XY: 727166
GnomAD4 genome AF: 0.000249 AC: 38AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74482
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 19, 2021 | In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge - |
Succinate-semialdehyde dehydrogenase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at