chr11-63598151-G-T

Position:

• chr11-63598151-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001128203.2(PLAAT3):​c.28C>A​(p.Pro10Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PLAAT3 NM_001128203.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.11

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]

ACMG classification

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=0.33949766).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLAAT3	NM_001128203.2	c.28C>A	p.Pro10Thr	missense_variant	3/5	ENST00000415826.3
PLAAT3	NM_007069.3	c.28C>A	p.Pro10Thr	missense_variant	2/4
PLAAT3	XM_011544741.2	c.73C>A	p.Pro25Thr	missense_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLAAT3	ENST00000415826.3	c.28C>A	p.Pro10Thr	missense_variant	3/5	2	NM_001128203.2	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 10, 2022

The c.28C>A (p.P10T) alteration is located in exon 2 (coding exon 2) of the PLA2G16 gene. This alteration results from a C to A substitution at nucleotide position 28, causing the proline (P) at amino acid position 10 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.074	T
BayesDel_noAF	Benign	-0.34
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.13	T;.;T
Eigen	Benign	0.14
Eigen_PC	Benign	0.082
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.93	.;D;D
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.34	T;T;T
MetaSVM	Benign	-0.99	T
MutationTaster	Benign	0.83	N;N
PrimateAI	Benign	0.37	T
PROVEAN	Pathogenic	-4.6	D;.;D
REVEL	Benign	0.16
Sift	Benign	0.053	T;.;T
Sift4G	Benign	0.082	T;.;T
Polyphen		0.91	P;.;P
Vest4		0.44
MutPred		0.39		Gain of phosphorylation at P10 (P = 0.0483);.;Gain of phosphorylation at P10 (P = 0.0483);
MVP		0.62
MPC		0.66
ClinPred		0.89	D
GERP RS		4.1
Varity_R		0.29
gMVP		0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-63365623;