1-56541867-T-C

Position:

• chr1-56541867-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003713.5(PLPP3):​c.140-4755A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,582 control chromosomes in the GnomAD database, including 14,447 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 0.43 (14447 hom., cov: 30)
• Consequence: PLPP3 NM_003713.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

Genes affected

PLPP3 (HGNC:9229): (phospholipid phosphatase 3) The protein encoded by this gene is a member of the phosphatidic acid phosphatase (PAP) family. PAPs convert phosphatidic acid to diacylglycerol, and function in de novo synthesis of glycerolipids as well as in receptor-activated signal transduction mediated by phospholipase D. This protein is a membrane glycoprotein localized at the cell plasma membrane. It has been shown to actively hydrolyze extracellular lysophosphatidic acid and short-chain phosphatidic acid. The expression of this gene is found to be enhanced by epidermal growth factor in Hela cells. [provided by RefSeq, Mar 2010]

PLPP3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLPP3	NM_003713.5	c.140-4755A>G		intron_variant		ENST00000371250.4	NP_003704.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLPP3	ENST00000371250.4	c.140-4755A>G		intron_variant		1	NM_003713.5	ENSP00000360296.3
PLPP3	ENST00000461655.1	n.242-4755A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64385 AN: 151466 Hom.: 14412 Cov.: 30

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.425 AC: 64472 AN: 151582 Hom.: 14447 Cov.: 30 AF XY: 0.426 AC XY: 31548 AN XY: 74018

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.408

Alfa AF: 0.360 Hom.: 19475

Bravo AF: 0.444

Asia WGS AF: 0.526 AC: 1830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.62

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

LitVar

Other links and lift over

dbSNP: rs1930760; hg19: chr1-57007539;