NM_001030059.3:c.165+3176C>T

Variant names:

• chr10-120507102-C-T
• rs1571099
• NM_001030059.3:c.165+3176C>T

Variant summary

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

The NM_001030059.3(PLPP4):​c.165+3176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,284 control chromosomes in the GnomAD database, including 70,601 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 0.96 (70601 hom., cov: 32)
• Consequence: PLPP4 NM_001030059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 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.165+3176C>T		intron	N/A	NP_001025230.1	Q5VZY2-1
	PLPP4	NM_001318167.2		c.165+3176C>T		intron	N/A	NP_001305096.1	Q5VZY2-2
	PLPP4	NM_001318166.2		c.165+3176C>T		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.165+3176C>T		intron	N/A	ENSP00000381302.1	Q5VZY2-1
	PLPP4	ENST00000369073.3	TSL:5	n.135+3176C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146378 AN: 152166 Hom.: 70557 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.970

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

GnomAD4 genome AF: 0.962 AC: 146481 AN: 152284 Hom.: 70601 Cov.: 32 AF XY: 0.964 AC XY: 71755 AN XY: 74472

African (AFR) AF: 0.888 AC: 36888 AN: 41518

American (AMR) AF: 0.978 AC: 14962 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.998 AC: 3465 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5188 AN: 5188

South Asian (SAS) AF: 0.997 AC: 4813 AN: 4828

European-Finnish (FIN) AF: 0.999 AC: 10610 AN: 10620

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.989 AC: 67304 AN: 68040

Other (OTH) AF: 0.970 AC: 2049 AN: 2112

Alfa AF: 0.976 Hom.: 28093

Bravo AF: 0.957

Asia WGS AF: 0.992 AC: 3452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.12
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: rs1571099; hg19: chr10-122266614;