chr10-50243257-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_019893.4(ASAH2):c.455G>A(p.Arg152Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,816 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 (★).
Frequency
Consequence
NM_019893.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ASAH2 | ENST00000682911.1 | c.455G>A | p.Arg152Gln | missense_variant | Exon 4 of 21 | NM_019893.4 | ENSP00000506746.1 | |||
ASAH2 | ENST00000395526.9 | c.455G>A | p.Arg152Gln | missense_variant | Exon 5 of 22 | 1 | ENSP00000378897.3 | |||
ASAH2 | ENST00000329428.10 | c.398G>A | p.Arg133Gln | missense_variant | Exon 3 of 19 | 1 | ENSP00000329886.6 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251278Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135798
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461816Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727210
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.455G>A (p.R152Q) alteration is located in exon 3 (coding exon 3) of the ASAH2 gene. This alteration results from a G to A substitution at nucleotide position 455, causing the arginine (R) at amino acid position 152 to be replaced by a glutamine (Q). 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