rs1130737
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000693.4(ALDH1A3):āc.43A>Gā(p.Arg15Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00859 in 1,472,488 control chromosomes in the GnomAD database, including 81 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_000693.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH1A3 | NM_000693.4 | c.43A>G | p.Arg15Gly | missense_variant | 1/13 | ENST00000329841.10 | |
ALDH1A3 | NM_001293815.2 | c.43A>G | p.Arg15Gly | missense_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH1A3 | ENST00000329841.10 | c.43A>G | p.Arg15Gly | missense_variant | 1/13 | 1 | NM_000693.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00570 AC: 865AN: 151776Hom.: 7 Cov.: 33
GnomAD3 exomes AF: 0.00463 AC: 389AN: 84108Hom.: 0 AF XY: 0.00455 AC XY: 216AN XY: 47456
GnomAD4 exome AF: 0.00892 AC: 11785AN: 1320604Hom.: 74 Cov.: 30 AF XY: 0.00861 AC XY: 5601AN XY: 650560
GnomAD4 genome ? AF: 0.00570 AC: 865AN: 151884Hom.: 7 Cov.: 33 AF XY: 0.00457 AC XY: 339AN XY: 74246
ClinVar
Submissions by phenotype
not provided Benign:5
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 28, 2020 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 09, 2016 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | ALDH1A3: BS2 - |
Isolated microphthalmia 8 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 24, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2023 | - - |
ALDH1A3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 30, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at