chr10-120547589-T-C

Position:

• chr10-120547589-T-C

Variant summary

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

The NM_001030059.3(PLPP4):​c.445+26494T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,200 control chromosomes in the GnomAD database, including 55,284 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 0.85 (55284 hom., cov: 32)
• Consequence: PLPP4 NM_001030059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLPP4	NM_001030059.3	c.445+26494T>C		intron_variant		ENST00000398250.6	NP_001025230.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLPP4	ENST00000398250.6	c.445+26494T>C		intron_variant		1	NM_001030059.3	ENSP00000381302.1
PLPP4	ENST00000369073.3	n.415+26494T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129108 AN: 152082 Hom.: 55264 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.849 AC: 129177 AN: 152200 Hom.: 55284 Cov.: 32 AF XY: 0.851 AC XY: 63302 AN XY: 74416

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.849

Alfa AF: 0.883 Hom.: 87137

Bravo AF: 0.838

Asia WGS AF: 0.880 AC: 3060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.63

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: rs4752432; hg19: chr10-122307101;