chr1-158944943-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152501.5(PYHIN1):c.1260G>T(p.Gln420His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000277 in 1,613,550 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. Q420R) 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.1260G>T | p.Gln420His | missense_variant | 7/9 | ENST00000368140.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYHIN1 | ENST00000368140.6 | c.1260G>T | p.Gln420His | missense_variant | 7/9 | 1 | NM_152501.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000115 AC: 29AN: 251140Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135746
GnomAD4 exome AF: 0.000296 AC: 433AN: 1461436Hom.: 0 Cov.: 30 AF XY: 0.000264 AC XY: 192AN XY: 727026
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.1260G>T (p.Q420H) alteration is located in exon 7 (coding exon 6) of the PYHIN1 gene. This alteration results from a G to T substitution at nucleotide position 1260, causing the glutamine (Q) at amino acid position 420 to be replaced by a histidine (H). 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