15-41840589-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001114633.2(PLA2G4B):c.148C>T(p.Arg50Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000143 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001114633.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLA2G4B | NM_001114633.2 | c.148C>T | p.Arg50Cys | missense_variant | Exon 3 of 20 | ENST00000458483.4 | NP_001108105.1 | |
JMJD7-PLA2G4B | NM_005090.4 | c.841C>T | p.Arg281Cys | missense_variant | Exon 8 of 25 | NP_005081.1 | ||
JMJD7-PLA2G4B | NM_001198588.2 | c.841C>T | p.Arg281Cys | missense_variant | Exon 8 of 24 | NP_001185517.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLA2G4B | ENST00000458483.4 | c.148C>T | p.Arg50Cys | missense_variant | Exon 3 of 20 | 2 | NM_001114633.2 | ENSP00000416610.1 | ||
JMJD7-PLA2G4B | ENST00000382448.8 | c.841C>T | p.Arg281Cys | missense_variant | Exon 8 of 25 | 2 | ENSP00000371886.4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248548Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134558
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461692Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727130
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.841C>T (p.R281C) alteration is located in exon 8 (coding exon 8) of the JMJD7-PLA2G4B gene. This alteration results from a C to T substitution at nucleotide position 841, causing the arginine (R) at amino acid position 281 to be replaced by a cysteine (C). 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