chr1-158943941-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152501.5(PYHIN1):c.1154T>C(p.Met385Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000355 in 1,608,616 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 (★).
Frequency
Consequence
NM_152501.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYHIN1 | NM_152501.5 | c.1154T>C | p.Met385Thr | missense_variant | 6/9 | ENST00000368140.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYHIN1 | ENST00000368140.6 | c.1154T>C | p.Met385Thr | missense_variant | 6/9 | 1 | NM_152501.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000168 AC: 42AN: 250618Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135444
GnomAD4 exome AF: 0.000377 AC: 549AN: 1456418Hom.: 0 Cov.: 31 AF XY: 0.000319 AC XY: 231AN XY: 724438
GnomAD4 genome ? AF: 0.000145 AC: 22AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2022 | The c.1154T>C (p.M385T) alteration is located in exon 6 (coding exon 5) of the PYHIN1 gene. This alteration results from a T to C substitution at nucleotide position 1154, causing the methionine (M) at amino acid position 385 to be replaced by a threonine (T). 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