10-120553624-A-G

Variant names:

• chr10-120553624-A-G
• rs10788102
• NM_001030059.3:c.446-21507A>G

Variant summary

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

The NM_001030059.3(PLPP4):​c.446-21507A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,916 control chromosomes in the GnomAD database, including 8,519 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 0.33 (8519 hom., cov: 33)
• Consequence: PLPP4 NM_001030059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 1 publications found

Genes affected

PLPP4 (HGNC:23531): (phospholipid phosphatase 4) Enables diacylglycerol diphosphate phosphatase activity; identical protein binding activity; and phosphatidate phosphatase activity. Involved in phospholipid dephosphorylation and regulation of calcium ion import. Predicted to be located in plasma membrane. Biomarker of breast cancer. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLPP4	NM_001030059.3	c.446-21507A>G		intron_variant	Intron 5 of 6	ENST00000398250.6	NP_001025230.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLPP4	ENST00000398250.6	c.446-21507A>G		intron_variant	Intron 5 of 6	1	NM_001030059.3	ENSP00000381302.1
PLPP4	ENST00000369073.3	n.416-21507A>G		intron_variant	Intron 5 of 6	5

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50647 AN: 151796 Hom.: 8519 Cov.: 33

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.334 AC: 50667 AN: 151916 Hom.: 8519 Cov.: 33 AF XY: 0.329 AC XY: 24406 AN XY: 74218

African (AFR) AF: 0.284 AC: 11792 AN: 41452

American (AMR) AF: 0.309 AC: 4725 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2017 AN: 5166

South Asian (SAS) AF: 0.189 AC: 913 AN: 4824

European-Finnish (FIN) AF: 0.330 AC: 3478 AN: 10524

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25137 AN: 67892

Other (OTH) AF: 0.342 AC: 723 AN: 2114

Alfa AF: 0.215 Hom.: 497

Bravo AF: 0.335

Asia WGS AF: 0.254 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.85
PhyloP100		-0.067
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: rs10788102; hg19: chr10-122313136; COSMIC: COSV64828267;