chr1-158944942-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152501.5(PYHIN1):c.1259A>G(p.Gln420Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,760 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. Q420H) 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.1259A>G | p.Gln420Arg | missense_variant | 7/9 | ENST00000368140.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYHIN1 | ENST00000368140.6 | c.1259A>G | p.Gln420Arg | missense_variant | 7/9 | 1 | NM_152501.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251202Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135766
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461552Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 727078
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.1259A>G (p.Q420R) alteration is located in exon 7 (coding exon 6) of the PYHIN1 gene. This alteration results from a A to G substitution at nucleotide position 1259, causing the glutamine (Q) at amino acid position 420 to be replaced by an arginine (R). 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