rs104894550
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP3_StrongPP5_Moderate
The NM_000049.4(ASPA):c.692A>G(p.Tyr231Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,460,970 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 Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y231H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000049.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASPA | NM_000049.4 | c.692A>G | p.Tyr231Cys | missense_variant | 5/6 | ENST00000263080.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASPA | ENST00000263080.3 | c.692A>G | p.Tyr231Cys | missense_variant | 5/6 | 1 | NM_000049.4 | P1 | |
ASPA | ENST00000456349.6 | c.692A>G | p.Tyr231Cys | missense_variant | 6/7 | 1 | P1 | ||
SPATA22 | ENST00000541913.5 | c.-74+19005T>C | intron_variant | 2 | |||||
SPATA22 | ENST00000570318.1 | c.-74+19204T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251424Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135876
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460970Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 726874
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Spongy degeneration of central nervous system Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Centogene AG - the Rare Disease Company | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 26, 1999 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at