11-63606176-C-T

Variant names:

• chr11-63606176-C-T
• rs2030731
• NM_001128203.2:c.15+7824G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001128203.2(PLAAT3):​c.15+7824G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,050 control chromosomes in the GnomAD database, including 6,307 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (6307 hom., cov: 31)
• Consequence: PLAAT3 NM_001128203.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569
• Publications: 13 publications found

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]

PLAAT3 Gene-Disease associations (from GenCC):

• lipodystrophy, familial partial, type 9

  Inheritance: AR Classification: LIMITED Submitted by: G2P, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLAAT3	NM_001128203.2	c.15+7824G>A		intron_variant	Intron 2 of 4	ENST00000415826.3	NP_001121675.1
PLAAT3	NM_007069.3	c.15+7824G>A		intron_variant	Intron 1 of 3		NP_009000.2
PLAAT3	XM_011544741.2	c.61-8013G>A		intron_variant	Intron 1 of 3		XP_011543043.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLAAT3	ENST00000415826.3	c.15+7824G>A		intron_variant	Intron 2 of 4	2	NM_001128203.2	ENSP00000389124.1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39596 AN: 151932 Hom.: 6302 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.291

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.261 AC: 39616 AN: 152050 Hom.: 6307 Cov.: 31 AF XY: 0.264 AC XY: 19635 AN XY: 74330

African (AFR) AF: 0.100 AC: 4164 AN: 41496

American (AMR) AF: 0.399 AC: 6086 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3470

East Asian (EAS) AF: 0.589 AC: 3035 AN: 5150

South Asian (SAS) AF: 0.246 AC: 1188 AN: 4826

European-Finnish (FIN) AF: 0.286 AC: 3021 AN: 10558

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19964 AN: 67980

Other (OTH) AF: 0.288 AC: 605 AN: 2102

Alfa AF: 0.282 Hom.: 4739

Bravo AF: 0.272

Asia WGS AF: 0.376 AC: 1307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.87
PhyloP100		0.57
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2030731; hg19: chr11-63373648;