22-21939563-GTCC-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_014634.4(PPM1F):c.321_323delGGA(p.Glu107del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00014 in 1,581,938 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014634.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPM1F | NM_014634.4 | c.321_323delGGA | p.Glu107del | disruptive_inframe_deletion | Exon 3 of 8 | ENST00000263212.10 | NP_055449.1 | |
PPM1F | NM_001410836.1 | c.-184_-182delGGA | 5_prime_UTR_variant | Exon 2 of 7 | NP_001397765.1 | |||
PPM1F-AS1 | NR_147620.1 | n.1336_1338delCTC | non_coding_transcript_exon_variant | Exon 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000440 AC: 67AN: 152164Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000814 AC: 16AN: 196490Hom.: 0 AF XY: 0.0000573 AC XY: 6AN XY: 104786
GnomAD4 exome AF: 0.000107 AC: 153AN: 1429656Hom.: 0 AF XY: 0.000107 AC XY: 76AN XY: 707968
GnomAD4 genome AF: 0.000453 AC: 69AN: 152282Hom.: 1 Cov.: 32 AF XY: 0.000322 AC XY: 24AN XY: 74452
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.321_323del, results in the deletion of 1 amino acid(s) of the PPM1F protein (p.Glu107del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs749703356, gnomAD 0.09%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with PPM1F-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at