1-186870523-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_024420.3(PLA2G4A):c.115+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00022 in 1,591,270 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024420.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLA2G4A | ENST00000367466.4 | c.115+7G>A | splice_region_variant, intron_variant | Intron 3 of 17 | 1 | NM_024420.3 | ENSP00000356436.3 | |||
PLA2G4A | ENST00000466600.1 | n.184+7G>A | splice_region_variant, intron_variant | Intron 2 of 6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000272 AC: 68AN: 249906Hom.: 0 AF XY: 0.000326 AC XY: 44AN XY: 135008
GnomAD4 exome AF: 0.000222 AC: 320AN: 1439118Hom.: 0 Cov.: 27 AF XY: 0.000248 AC XY: 178AN XY: 717170
GnomAD4 genome AF: 0.000197 AC: 30AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74396
ClinVar
Submissions by phenotype
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at