chr10-120586831-T-C

Variant names:

• chr10-120586831-T-C
• rs3816785
• NM_001030059.3:c.617-2472T>C

Variant summary

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

The NM_001030059.3(PLPP4):​c.617-2472T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,886 control chromosomes in the GnomAD database, including 3,147 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 0.20 (3147 hom., cov: 31)
• Consequence: PLPP4 NM_001030059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001030059.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLPP4	NM_001030059.3	MANE Select	c.617-2472T>C		intron	N/A	NP_001025230.1	Q5VZY2-1
	PLPP4	NM_001318167.2		c.428-2472T>C		intron	N/A	NP_001305096.1	Q5VZY2-2
	PLPP4	NM_001318166.2		c.492-2472T>C		intron	N/A	NP_001305095.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLPP4	ENST00000398250.6	TSL:1 MANE Select	c.617-2472T>C		intron	N/A	ENSP00000381302.1	Q5VZY2-1
	PLPP4	ENST00000369073.3	TSL:5	n.587-2472T>C		intron	N/A
	PLPP4	ENST00000496437.1	TSL:3	n.115-428T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30437 AN: 151770 Hom.: 3146 Cov.: 31

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.200 AC: 30443 AN: 151886 Hom.: 3147 Cov.: 31 AF XY: 0.204 AC XY: 15169 AN XY: 74268

African (AFR) AF: 0.168 AC: 6937 AN: 41390

American (AMR) AF: 0.222 AC: 3393 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3466

East Asian (EAS) AF: 0.234 AC: 1210 AN: 5162

South Asian (SAS) AF: 0.170 AC: 817 AN: 4800

European-Finnish (FIN) AF: 0.287 AC: 3022 AN: 10544

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.200 AC: 13596 AN: 67948

Other (OTH) AF: 0.200 AC: 421 AN: 2106

Alfa AF: 0.198 Hom.: 6101

Bravo AF: 0.193

Asia WGS AF: 0.158 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.26
PhyloP100		-0.53
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: rs3816785; hg19: chr10-122346343;