2-159951564-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_007366.5(PLA2R1):c.3316G>A(p.Gly1106Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 1,533,322 control chromosomes in the GnomAD database, including 163,322 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_007366.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLA2R1 | NM_007366.5 | c.3316G>A | p.Gly1106Ser | missense_variant | 24/30 | ENST00000283243.13 | NP_031392.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLA2R1 | ENST00000283243.13 | c.3316G>A | p.Gly1106Ser | missense_variant | 24/30 | 1 | NM_007366.5 | ENSP00000283243 | P1 | |
PLA2R1 | ENST00000392771.1 | c.3316G>A | p.Gly1106Ser | missense_variant | 24/27 | 1 | ENSP00000376524 |
Frequencies
GnomAD3 genomes AF: 0.366 AC: 55649AN: 151944Hom.: 12836 Cov.: 32
GnomAD3 exomes AF: 0.397 AC: 99601AN: 250600Hom.: 22908 AF XY: 0.398 AC XY: 53916AN XY: 135462
GnomAD4 exome AF: 0.452 AC: 624656AN: 1381260Hom.: 150486 Cov.: 24 AF XY: 0.447 AC XY: 308988AN XY: 691746
GnomAD4 genome AF: 0.366 AC: 55656AN: 152062Hom.: 12836 Cov.: 32 AF XY: 0.367 AC XY: 27290AN XY: 74316
ClinVar
Submissions by phenotype
Atypical hemolytic-uremic syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Oct 05, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at