rs12566304

Variant names:

• chr1-56570684-C-A
• rs12566304
• NM_003713.5:c.139+8194G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-56570684-C-A
• chr1-56570684-C-G
• chr1-56570684-C-T

Variant summary

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

The NM_003713.5(PLPP3):​c.139+8194G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,042 control chromosomes in the GnomAD database, including 6,812 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 0.28 (6812 hom., cov: 32)
• Consequence: PLPP3 NM_003713.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLPP3	NM_003713.5	c.139+8194G>T		intron_variant	Intron 1 of 5	ENST00000371250.4	NP_003704.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLPP3	ENST00000371250.4	c.139+8194G>T		intron_variant	Intron 1 of 5	1	NM_003713.5	ENSP00000360296.3
PLPP3	ENST00000461655.1	n.242-33572G>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42476 AN: 151924 Hom.: 6812 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.279 AC: 42468 AN: 152042 Hom.: 6812 Cov.: 32 AF XY: 0.280 AC XY: 20811 AN XY: 74310

African (AFR) AF: 0.136 AC: 5636 AN: 41492

American (AMR) AF: 0.254 AC: 3889 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3472

East Asian (EAS) AF: 0.149 AC: 769 AN: 5178

South Asian (SAS) AF: 0.166 AC: 803 AN: 4826

European-Finnish (FIN) AF: 0.404 AC: 4251 AN: 10534

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24741 AN: 67942

Other (OTH) AF: 0.311 AC: 657 AN: 2110

Alfa AF: 0.199 Hom.: 502

Bravo AF: 0.264

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.6
DANN	Benign	0.80
PhyloP100		-0.31
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: rs12566304; hg19: chr1-57036357; COSMIC: COSV64838988;