15-100905610-A-G
Variant summary
Our verdict is Benign. The variant received -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_000693.4(ALDH1A3):c.1156A>G(p.Met386Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0423 in 1,613,692 control chromosomes in the GnomAD database, including 4,098 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_000693.4 missense
Scores
Clinical Significance
Conservation
Publications
Genome browser will be placed here
ACMG classification
Our verdict: Benign. The variant received -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALDH1A3 | NM_000693.4 | c.1156A>G | p.Met386Val | missense_variant | Exon 10 of 13 | ENST00000329841.10 | NP_000684.2 | |
ALDH1A3 | NM_001293815.2 | c.835A>G | p.Met279Val | missense_variant | Exon 7 of 10 | NP_001280744.1 | ||
ALDH1A3-AS1 | NR_135827.1 | n.481-9544T>C | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.105 AC: 16010AN: 152092Hom.: 1755 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0539 AC: 13524AN: 250724 AF XY: 0.0507 show subpopulations
GnomAD4 exome AF: 0.0357 AC: 52208AN: 1461484Hom.: 2332 Cov.: 31 AF XY: 0.0356 AC XY: 25915AN XY: 727028 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.105 AC: 16055AN: 152208Hom.: 1766 Cov.: 32 AF XY: 0.106 AC XY: 7898AN XY: 74420 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
not specified Benign:1
- -
Isolated microphthalmia 8 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at