15-57955233-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_003888.4(ALDH1A2):āc.1521G>Cā(p.Lys507Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,872 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 (ā ).
Frequency
Consequence
NM_003888.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALDH1A2 | NM_003888.4 | c.1521G>C | p.Lys507Asn | missense_variant | Exon 13 of 13 | ENST00000249750.9 | NP_003879.2 | |
ALDH1A2 | NM_001206897.2 | c.1458G>C | p.Lys486Asn | missense_variant | Exon 14 of 14 | NP_001193826.1 | ||
ALDH1A2 | NM_170696.3 | c.1407G>C | p.Lys469Asn | missense_variant | Exon 12 of 12 | NP_733797.1 | ||
ALDH1A2 | NM_170697.3 | c.1233G>C | p.Lys411Asn | missense_variant | Exon 11 of 11 | NP_733798.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250380Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135414
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461872Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727242
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1521G>C (p.K507N) alteration is located in exon 13 (coding exon 13) of the ALDH1A2 gene. This alteration results from a G to C substitution at nucleotide position 1521, causing the lysine (K) at amino acid position 507 to be replaced by an asparagine (N). 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