chr15-100885290-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_000693.4(ALDH1A3):c.123C>G(p.His41Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0002 in 1,613,388 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000693.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH1A3 | NM_000693.4 | c.123C>G | p.His41Gln | missense_variant | 2/13 | ENST00000329841.10 | |
ALDH1A3 | NM_001293815.2 | c.123C>G | p.His41Gln | missense_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH1A3 | ENST00000329841.10 | c.123C>G | p.His41Gln | missense_variant | 2/13 | 1 | NM_000693.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00110 AC: 167AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000239 AC: 60AN: 251446Hom.: 1 AF XY: 0.000206 AC XY: 28AN XY: 135902
GnomAD4 exome AF: 0.000106 AC: 155AN: 1461120Hom.: 0 Cov.: 30 AF XY: 0.0000908 AC XY: 66AN XY: 726918
GnomAD4 genome ? AF: 0.00110 AC: 167AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.00102 AC XY: 76AN XY: 74448
ClinVar
Submissions by phenotype
ALDH1A3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 11, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Isolated microphthalmia 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 12, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at