1-156236427-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007221.4(PMF1):c.508C>T(p.Arg170Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000948 in 1,614,076 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007221.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PMF1 | ENST00000368277.3 | c.508C>T | p.Arg170Trp | missense_variant | Exon 4 of 5 | 1 | NM_007221.4 | ENSP00000357260.3 | ||
PMF1-BGLAP | ENST00000490491.5 | c.508C>T | p.Arg170Trp | missense_variant | Exon 4 of 7 | 2 | ENSP00000475561.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250684Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135630
GnomAD4 exome AF: 0.0000951 AC: 139AN: 1461802Hom.: 0 Cov.: 31 AF XY: 0.0000976 AC XY: 71AN XY: 727202
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74460
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.514C>T (p.R172W) alteration is located in exon 4 (coding exon 4) of the PMF1 gene. This alteration results from a C to T substitution at nucleotide position 514, causing the arginine (R) at amino acid position 172 to be replaced by a tryptophan (W). 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