rs777936704
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_000049.4(ASPA):c.428T>C(p.Ile143Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000691 in 1,447,592 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I143V) has been classified as Uncertain significance.
Frequency
Consequence
NM_000049.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASPA | NM_000049.4 | c.428T>C | p.Ile143Thr | missense_variant | 2/6 | ENST00000263080.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASPA | ENST00000263080.3 | c.428T>C | p.Ile143Thr | missense_variant | 2/6 | 1 | NM_000049.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000423 AC: 1AN: 236462Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 127732
GnomAD4 exome AF: 6.91e-7 AC: 1AN: 1447592Hom.: 0 Cov.: 29 AF XY: 0.00000139 AC XY: 1AN XY: 719684
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Spongy degeneration of central nervous system Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Apr 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at