1-56497354-C-T

Variant names:

• chr1-56497354-C-T
• rs11206831
• NM_003713.5:c.811-678G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000284686 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PLPP3	NM_003713.5	c.811-678G>A		intron_variant	Intron 5 of 5	ENST00000371250.4	NP_003704.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLPP3	ENST00000371250.4	c.811-678G>A		intron_variant	Intron 5 of 5	1	NM_003713.5	ENSP00000360296.3
ENSG00000284686	ENST00000642129.1	n.454-678G>A		intron_variant	Intron 3 of 5			ENSP00000492927.1

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

African (AFR) AF: 0.0449 AC: 1864 AN: 41510

American (AMR) AF: 0.158 AC: 2418 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3466

East Asian (EAS) AF: 0.0612 AC: 317 AN: 5180

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4826

European-Finnish (FIN) AF: 0.274 AC: 2891 AN: 10556

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15894 AN: 68000

Other (OTH) AF: 0.180 AC: 380 AN: 2114

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
PhyloP100		0.91
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: rs11206831; hg19: chr1-56963026;