chr1-158942029-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_152501.5(PYHIN1):c.632G>A(p.Arg211Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000323 in 1,612,496 control chromosomes in the GnomAD database, including 3 homozygotes. 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 (★).
Frequency
Consequence
NM_152501.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYHIN1 | NM_152501.5 | c.632G>A | p.Arg211Gln | missense_variant | 5/9 | ENST00000368140.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYHIN1 | ENST00000368140.6 | c.632G>A | p.Arg211Gln | missense_variant | 5/9 | 1 | NM_152501.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000302 AC: 46AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000436 AC: 109AN: 250018Hom.: 1 AF XY: 0.000451 AC XY: 61AN XY: 135182
GnomAD4 exome AF: 0.000325 AC: 475AN: 1460260Hom.: 3 Cov.: 31 AF XY: 0.000332 AC XY: 241AN XY: 726320
GnomAD4 genome ? AF: 0.000302 AC: 46AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2021 | The c.632G>A (p.R211Q) alteration is located in exon 5 (coding exon 4) of the PYHIN1 gene. This alteration results from a G to A substitution at nucleotide position 632, causing the arginine (R) at amino acid position 211 to be replaced by a glutamine (Q). 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