chr16-72122957-G-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_031293.3(PMFBP1):c.2725C>T(p.Arg909Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000075 in 1,613,354 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_031293.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PMFBP1 | NM_031293.3 | c.2725C>T | p.Arg909Ter | stop_gained | 19/21 | ENST00000237353.15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PMFBP1 | ENST00000237353.15 | c.2725C>T | p.Arg909Ter | stop_gained | 19/21 | 1 | NM_031293.3 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152094Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000187 AC: 47AN: 250910Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135654
GnomAD4 exome AF: 0.0000691 AC: 101AN: 1461142Hom.: 0 Cov.: 32 AF XY: 0.0000619 AC XY: 45AN XY: 726904
GnomAD4 genome AF: 0.000131 AC: 20AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74404
ClinVar
Submissions by phenotype
Spermatogenic failure 31 Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 30, 2022 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 07, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at