chr19-49461912-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_153329.4(ALDH16A1):c.788C>A(p.Ala263Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,580,492 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A263T) has been classified as Uncertain significance.
Frequency
Consequence
NM_153329.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH16A1 | NM_153329.4 | c.788C>A | p.Ala263Glu | missense_variant | 7/17 | ENST00000293350.9 | |
ALDH16A1 | XM_011526441.1 | c.701C>A | p.Ala234Glu | missense_variant | 7/17 | ||
ALDH16A1 | XM_047438163.1 | c.701C>A | p.Ala234Glu | missense_variant | 8/18 | ||
ALDH16A1 | NM_001145396.2 | c.759+112C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH16A1 | ENST00000293350.9 | c.788C>A | p.Ala263Glu | missense_variant | 7/17 | 1 | NM_153329.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000790 AC: 12AN: 151808Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000108 AC: 21AN: 193984Hom.: 0 AF XY: 0.000104 AC XY: 11AN XY: 105464
GnomAD4 exome AF: 0.000130 AC: 186AN: 1428684Hom.: 0 Cov.: 60 AF XY: 0.000114 AC XY: 81AN XY: 708258
GnomAD4 genome ? AF: 0.0000790 AC: 12AN: 151808Hom.: 0 Cov.: 33 AF XY: 0.0000539 AC XY: 4AN XY: 74152
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 09, 2023 | The c.788C>A (p.A263E) alteration is located in exon 7 (coding exon 7) of the ALDH16A1 gene. This alteration results from a C to A substitution at nucleotide position 788, causing the alanine (A) at amino acid position 263 to be replaced by a glutamic acid (E). 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