rs11206831

Positions:

• chr1-56497354-C-T

Variant summary

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

The NM_003713.5(PLPP3):​c.811-678G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,140 control chromosomes in the GnomAD database, including 2,811 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 0.17 (2811 hom., cov: 33)
• Consequence: PLPP3 NM_003713.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.913

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLPP3	NM_003713.5	c.811-678G>A		intron_variant		ENST00000371250.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLPP3	ENST00000371250.4	c.811-678G>A		intron_variant		1	NM_003713.5	P1
PLPP3	ENST00000459962.1	n.1797-678G>A		intron_variant, non_coding_transcript_variant		2
PLPP3	ENST00000472957.1	n.296-678G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25959 AN: 152022 Hom.: 2812 Cov.: 33

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.171 AC: 25972 AN: 152140 Hom.: 2811 Cov.: 33 AF XY: 0.171 AC XY: 12711 AN XY: 74346

Gnomad4 AFR AF: 0.0449

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.0612

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.180

Alfa AF: 0.199 Hom.: 441

Bravo AF: 0.155

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.6
DANN	Benign	0.78

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: rs11206831; hg19: chr1-56963026;