chr1-158942388-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152501.5(PYHIN1):c.991A>T(p.Met331Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000139 in 1,442,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign 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. M331I) has been classified as Uncertain significance.
Frequency
Consequence
NM_152501.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYHIN1 | NM_152501.5 | c.991A>T | p.Met331Leu | missense_variant | 5/9 | ENST00000368140.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYHIN1 | ENST00000368140.6 | c.991A>T | p.Met331Leu | missense_variant | 5/9 | 1 | NM_152501.5 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1442080Hom.: 0 Cov.: 30 AF XY: 0.00000140 AC XY: 1AN XY: 716256
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
PYHIN1-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 03, 2024 | The PYHIN1 c.991A>T variant is predicted to result in the amino acid substitution p.Met331Leu. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at