15-42142584-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_213600.4(PLA2G4F):c.2273C>G(p.Pro758Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,613,960 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 Uncertain significance (★).
Frequency
Consequence
NM_213600.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLA2G4F | NM_213600.4 | c.2273C>G | p.Pro758Arg | missense_variant | Exon 19 of 20 | ENST00000397272.7 | NP_998765.3 | |
PLA2G4F | NR_033151.2 | n.2287C>G | non_coding_transcript_exon_variant | Exon 18 of 19 | ||||
PLA2G4F | XR_931785.1 | n.*42C>G | downstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251294Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135842
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461820Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727218
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2273C>G (p.P758R) alteration is located in exon 19 (coding exon 19) of the PLA2G4F gene. This alteration results from a C to G substitution at nucleotide position 2273, causing the proline (P) at amino acid position 758 to be replaced by an arginine (R). 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