rs1571101

Variant names:

• chr10-120510905-G-A
• rs1571101
• NM_001030059.3:c.166-3006G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-120510905-G-A
• chr10-120510905-G-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.166-3006G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 152,052 control chromosomes in the GnomAD database, including 15,078 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 0.44 (15078 hom., cov: 32)
• Consequence: PLPP4 NM_001030059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.798
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLPP4	NM_001030059.3	c.166-3006G>A		intron_variant	Intron 2 of 6	ENST00000398250.6	NP_001025230.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLPP4	ENST00000398250.6	c.166-3006G>A		intron_variant	Intron 2 of 6	1	NM_001030059.3	ENSP00000381302.1
PLPP4	ENST00000369073.3	n.136-3006G>A		intron_variant	Intron 2 of 6	5

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67211 AN: 151934 Hom.: 15070 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.442 AC: 67259 AN: 152052 Hom.: 15078 Cov.: 32 AF XY: 0.447 AC XY: 33198 AN XY: 74298

African (AFR) AF: 0.389 AC: 16109 AN: 41464

American (AMR) AF: 0.435 AC: 6647 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1368 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1746 AN: 5144

South Asian (SAS) AF: 0.594 AC: 2852 AN: 4802

European-Finnish (FIN) AF: 0.465 AC: 4923 AN: 10586

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32031 AN: 67990

Other (OTH) AF: 0.425 AC: 898 AN: 2112

Alfa AF: 0.455 Hom.: 20491

Bravo AF: 0.435

Asia WGS AF: 0.493 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.58
PhyloP100		0.80
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: rs1571101; hg19: chr10-122270417;