chr1-19978433-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_001395463.1(PLA2G2A):c.132C>T(p.Tyr44Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 1,611,986 control chromosomes in the GnomAD database, including 36,779 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001395463.1 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLA2G2A | NM_001395463.1 | c.132C>T | p.Tyr44Tyr | synonymous_variant | Exon 3 of 5 | ENST00000482011.3 | NP_001382392.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.176 AC: 26744AN: 152026Hom.: 2789 Cov.: 32
GnomAD3 exomes AF: 0.176 AC: 43563AN: 246998Hom.: 4668 AF XY: 0.178 AC XY: 23964AN XY: 134344
GnomAD4 exome AF: 0.208 AC: 304039AN: 1459840Hom.: 33985 Cov.: 36 AF XY: 0.207 AC XY: 150044AN XY: 726290
GnomAD4 genome AF: 0.176 AC: 26767AN: 152146Hom.: 2794 Cov.: 32 AF XY: 0.173 AC XY: 12894AN XY: 74378
ClinVar
Submissions by phenotype
PLA2G2A-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at