chr15-58065656-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_003888.4(ALDH1A2):c.-6G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0401 in 1,579,938 control chromosomes in the GnomAD database, including 1,428 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_003888.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALDH1A2 | NM_003888.4 | c.-6G>A | 5_prime_UTR_variant | Exon 1 of 13 | ENST00000249750.9 | NP_003879.2 | ||
ALDH1A2 | NM_001206897.2 | c.-166G>A | 5_prime_UTR_variant | Exon 1 of 14 | NP_001193826.1 | |||
ALDH1A2 | NM_170696.3 | c.-6G>A | 5_prime_UTR_variant | Exon 1 of 12 | NP_733797.1 | |||
ALDH1A2-AS1 | NR_147215.1 | n.432C>T | non_coding_transcript_exon_variant | Exon 1 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0304 AC: 4621AN: 152006Hom.: 105 Cov.: 32
GnomAD3 exomes AF: 0.0336 AC: 6763AN: 201018Hom.: 151 AF XY: 0.0340 AC XY: 3695AN XY: 108816
GnomAD4 exome AF: 0.0411 AC: 58665AN: 1427814Hom.: 1323 Cov.: 29 AF XY: 0.0404 AC XY: 28563AN XY: 707292
GnomAD4 genome AF: 0.0304 AC: 4621AN: 152124Hom.: 105 Cov.: 32 AF XY: 0.0298 AC XY: 2215AN XY: 74388
ClinVar
Submissions by phenotype
ALDH1A2-related disorder Benign:1
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