rs35251510
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_003888.4(ALDH1A2):c.1254C>A(p.Ile418=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00301 in 1,613,738 control chromosomes in the GnomAD database, including 75 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003888.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH1A2 | NM_003888.4 | c.1254C>A | p.Ile418= | splice_region_variant, synonymous_variant | 11/13 | ENST00000249750.9 | |
ALDH1A2 | NM_001206897.2 | c.1191C>A | p.Ile397= | splice_region_variant, synonymous_variant | 12/14 | ||
ALDH1A2 | NM_170696.3 | c.1140C>A | p.Ile380= | splice_region_variant, synonymous_variant | 10/12 | ||
ALDH1A2 | NM_170697.3 | c.966C>A | p.Ile322= | splice_region_variant, synonymous_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH1A2 | ENST00000249750.9 | c.1254C>A | p.Ile418= | splice_region_variant, synonymous_variant | 11/13 | 1 | NM_003888.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00632 AC: 961AN: 152144Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00253 AC: 634AN: 250782Hom.: 1 AF XY: 0.00214 AC XY: 290AN XY: 135584
GnomAD4 exome AF: 0.00267 AC: 3898AN: 1461476Hom.: 67 Cov.: 32 AF XY: 0.00256 AC XY: 1860AN XY: 727088
GnomAD4 genome AF: 0.00633 AC: 964AN: 152262Hom.: 8 Cov.: 32 AF XY: 0.00594 AC XY: 442AN XY: 74438
ClinVar
Submissions by phenotype
ALDH1A2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at