5-55528158-A-G

Variant names:

• chr5-55528158-A-G
• rs1995039
• NM_003711.4:c.58+6414T>C

Variant summary

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

The NM_003711.4(PLPP1):​c.58+6414T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,112 control chromosomes in the GnomAD database, including 47,049 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 0.78 (47049 hom., cov: 31)
• Consequence: PLPP1 NM_003711.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

Genes affected

PLPP1 (HGNC:9228): (phospholipid phosphatase 1) The protein encoded by this gene is a member of the phosphatidic acid phosphatase (PAP) family. PAPs convert phosphatidic acid to diacylglycerol, and function in synthesis of glycerolipids and in phospholipase D-mediated signal transduction. This enzyme is an integral membrane glycoprotein that plays a role in the hydrolysis and uptake of lipids from extracellular space. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLPP1	NM_003711.4	c.58+6414T>C		intron_variant	Intron 1 of 5	ENST00000307259.9	NP_003702.2
PLPP1	NM_176895.3	c.58+6414T>C		intron_variant	Intron 1 of 5		NP_795714.1
PLPP1	XM_006714724.4	c.21+6414T>C		intron_variant	Intron 1 of 4		XP_006714787.1
PLPP1	NR_103485.2	n.393+6414T>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLPP1	ENST00000307259.9	c.58+6414T>C		intron_variant	Intron 1 of 5	1	NM_003711.4	ENSP00000302229.8
PLPP1	ENST00000264775.9	c.58+6414T>C		intron_variant	Intron 1 of 5	1		ENSP00000264775.5
PLPP1	ENST00000509667.5	n.58+6414T>C		intron_variant	Intron 1 of 4	5		ENSP00000425052.1
PLPP1	ENST00000515132.5	n.393+6414T>C		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118196 AN: 151996 Hom.: 47039 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.777 AC: 118243 AN: 152112 Hom.: 47049 Cov.: 31 AF XY: 0.776 AC XY: 57662 AN XY: 74344

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.787

Alfa AF: 0.817 Hom.: 7195

Bravo AF: 0.763

Asia WGS AF: 0.693 AC: 2408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.60

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: rs1995039; hg19: chr5-54823986;