15-57955213-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003888.4(ALDH1A2):c.1541C>T(p.Pro514Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000186 in 1,613,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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. P514A) has been classified as Uncertain significance.
Frequency
Consequence
NM_003888.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH1A2 | NM_003888.4 | c.1541C>T | p.Pro514Leu | missense_variant | 13/13 | ENST00000249750.9 | |
ALDH1A2 | NM_001206897.2 | c.1478C>T | p.Pro493Leu | missense_variant | 14/14 | ||
ALDH1A2 | NM_170696.3 | c.1427C>T | p.Pro476Leu | missense_variant | 12/12 | ||
ALDH1A2 | NM_170697.3 | c.1253C>T | p.Pro418Leu | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH1A2 | ENST00000249750.9 | c.1541C>T | p.Pro514Leu | missense_variant | 13/13 | 1 | NM_003888.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251024Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135704
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461860Hom.: 0 Cov.: 30 AF XY: 0.0000220 AC XY: 16AN XY: 727236
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.1541C>T (p.P514L) alteration is located in exon 13 (coding exon 13) of the ALDH1A2 gene. This alteration results from a C to T substitution at nucleotide position 1541, causing the proline (P) at amino acid position 514 to be replaced by a leucine (L). 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