15-42142015-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_213600.4(PLA2G4F):c.2519G>A(p.Arg840Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000164 in 1,613,910 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2G4F | NM_213600.4 | c.2519G>A | p.Arg840Gln | missense_variant | 20/20 | ENST00000397272.7 | |
PLA2G4F | NR_033151.2 | n.2533G>A | non_coding_transcript_exon_variant | 19/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2G4F | ENST00000397272.7 | c.2519G>A | p.Arg840Gln | missense_variant | 20/20 | 1 | NM_213600.4 | P1 | |
PLA2G4F | ENST00000290497.11 | c.*2263G>A | 3_prime_UTR_variant, NMD_transcript_variant | 19/19 | 1 | ||||
PLA2G4F | ENST00000562320.1 | c.*324G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 1 | ||||
PLA2G4F | ENST00000569985.5 | c.*1563G>A | 3_prime_UTR_variant, NMD_transcript_variant | 20/20 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000552 AC: 84AN: 152202Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251376Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135866
GnomAD4 exome AF: 0.000124 AC: 181AN: 1461708Hom.: 0 Cov.: 30 AF XY: 0.000118 AC XY: 86AN XY: 727154
GnomAD4 genome AF: 0.000552 AC: 84AN: 152202Hom.: 2 Cov.: 32 AF XY: 0.000578 AC XY: 43AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.2519G>A (p.R840Q) alteration is located in exon 20 (coding exon 20) of the PLA2G4F gene. This alteration results from a G to A substitution at nucleotide position 2519, causing the arginine (R) at amino acid position 840 to be replaced by a glutamine (Q). 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