17-19740351-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000691.5(ALDH3A1):c.934G>A(p.Ala312Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000691.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALDH3A1 | NM_000691.5 | c.934G>A | p.Ala312Thr | missense_variant | 7/11 | ENST00000225740.11 | NP_000682.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALDH3A1 | ENST00000225740.11 | c.934G>A | p.Ala312Thr | missense_variant | 7/11 | 1 | NM_000691.5 | ENSP00000225740 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250908Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135682
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461576Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727094
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.934G>A (p.A312T) alteration is located in exon 6 (coding exon 6) of the ALDH3A1 gene. This alteration results from a G to A substitution at nucleotide position 934, causing the alanine (A) at amino acid position 312 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at