rs2307279
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003706.3(PLA2G4C):c.112G>C(p.Ala38Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 1,610,406 control chromosomes in the GnomAD database, including 14,359 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003706.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2G4C | NM_003706.3 | c.112G>C | p.Ala38Pro | missense_variant | 3/17 | ENST00000599921.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2G4C | ENST00000599921.6 | c.112G>C | p.Ala38Pro | missense_variant | 3/17 | 1 | NM_003706.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.186 AC: 28289AN: 151926Hom.: 5525 Cov.: 30
GnomAD3 exomes AF: 0.109 AC: 27273AN: 250114Hom.: 3436 AF XY: 0.102 AC XY: 13827AN XY: 135252
GnomAD4 exome AF: 0.0675 AC: 98378AN: 1458362Hom.: 8819 Cov.: 30 AF XY: 0.0681 AC XY: 49404AN XY: 725624
GnomAD4 genome ? AF: 0.186 AC: 28342AN: 152044Hom.: 5540 Cov.: 30 AF XY: 0.184 AC XY: 13669AN XY: 74344
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at