11-63590334-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001128203.2(PLAAT3):c.153G>A(p.Met51Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,978 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000096 ( 1 hom. )
Consequence
PLAAT3
NM_001128203.2 missense
NM_001128203.2 missense
Scores
1
3
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.40
Genes affected
PLAAT3 (HGNC:17825): (phospholipase A and acyltransferase 3) Enables N-acyltransferase activity; phospholipase A1 activity; and phospholipase A2 activity. Involved in N-acylphosphatidylethanolamine metabolic process. Predicted to be located in several cellular components, including lysosome; nuclear envelope; and peroxisome. Predicted to be active in cytoplasm. Biomarker of seminoma. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.28131163).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLAAT3 | NM_001128203.2 | c.153G>A | p.Met51Ile | missense_variant | 4/5 | ENST00000415826.3 | |
PLAAT3 | NM_007069.3 | c.153G>A | p.Met51Ile | missense_variant | 3/4 | ||
PLAAT3 | XM_011544741.2 | c.198G>A | p.Met66Ile | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLAAT3 | ENST00000415826.3 | c.153G>A | p.Met51Ile | missense_variant | 4/5 | 2 | NM_001128203.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152244Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251184Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135762
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GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461616Hom.: 1 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 727120
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GnomAD4 genome AF: 0.0000328 AC: 5AN: 152362Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74508
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;.;N;D
REVEL
Benign
Sift
Benign
D;.;D;.
Sift4G
Benign
T;.;T;.
Polyphen
B;.;B;.
Vest4
MutPred
Loss of disorder (P = 0.0785);.;Loss of disorder (P = 0.0785);.;
MVP
MPC
ClinPred
T
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at