chr12-111783212-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000690.4(ALDH2):c.274C>A(p.Pro92Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000624 in 1,613,488 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P92A) has been classified as Uncertain significance.
Frequency
Consequence
NM_000690.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALDH2 | NM_000690.4 | c.274C>A | p.Pro92Thr | missense_variant | Exon 3 of 13 | ENST00000261733.7 | NP_000681.2 | |
ALDH2 | NM_001204889.2 | c.219+1190C>A | intron_variant | Intron 2 of 11 | NP_001191818.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALDH2 | ENST00000261733.7 | c.274C>A | p.Pro92Thr | missense_variant | Exon 3 of 13 | 1 | NM_000690.4 | ENSP00000261733.2 | ||
ENSG00000257767 | ENST00000546840.3 | c.262C>A | p.Pro88Thr | missense_variant | Exon 4 of 8 | 5 | ENSP00000450353.4 |
Frequencies
GnomAD3 genomes AF: 0.000677 AC: 103AN: 152242Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00307 AC: 768AN: 250046Hom.: 9 AF XY: 0.00217 AC XY: 294AN XY: 135266
GnomAD4 exome AF: 0.000619 AC: 904AN: 1461128Hom.: 9 Cov.: 31 AF XY: 0.000505 AC XY: 367AN XY: 726804
GnomAD4 genome AF: 0.000676 AC: 103AN: 152360Hom.: 1 Cov.: 32 AF XY: 0.000671 AC XY: 50AN XY: 74510
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at