rs1571500

Variant names:

• chr1-98920737-T-C
• rs1571500
• NM_001037317.2:c.798+1145A>G

Variant summary

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

The NM_001037317.2(PLPPR5):​c.798+1145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,182 control chromosomes in the GnomAD database, including 1,081 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 0.10 (1081 hom., cov: 31)
• Consequence: PLPPR5 NM_001037317.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87

Genes affected

PLPPR5 (HGNC:31703): (phospholipid phosphatase related 5) The protein encoded by this gene is a type 2 member of the phosphatidic acid phosphatase (PAP) family. All type 2 members of this protein family contain 6 transmembrane regions, and a consensus N-glycosylation site. PAPs convert phosphatidic acid to diacylglycerol, and function in de novo synthesis of glycerolipids as well as in receptor-activated signal transduction mediated by phospholipase D. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLPPR5	NM_001037317.2	c.798+1145A>G		intron_variant	Intron 4 of 5	ENST00000263177.5	NP_001032394.1
PLPPR5	NM_001010861.3	c.798+1145A>G		intron_variant	Intron 4 of 5		NP_001010861.1
PLPPR5	XM_011540838.4	c.750+1145A>G		intron_variant	Intron 5 of 6		XP_011539140.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLPPR5	ENST00000263177.5	c.798+1145A>G		intron_variant	Intron 4 of 5	1	NM_001037317.2	ENSP00000263177.4
PLPPR5	ENST00000370188.7	c.798+1145A>G		intron_variant	Intron 4 of 5	1		ENSP00000359207.3
PLPPR5	ENST00000672681.1	c.798+1145A>G		intron_variant	Intron 4 of 6			ENSP00000500930.1
PLPPR5	ENST00000696571.1	c.633+1145A>G		intron_variant	Intron 5 of 6			ENSP00000512726.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15639 AN: 152064 Hom.: 1077 Cov.: 31

Gnomad AFR AF: 0.0354

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.103 AC: 15656 AN: 152182 Hom.: 1081 Cov.: 31 AF XY: 0.107 AC XY: 7929 AN XY: 74392

Gnomad4 AFR AF: 0.0353

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.0830

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.114

Alfa AF: 0.116 Hom.: 701

Bravo AF: 0.106

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.6
DANN	Benign	0.87

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: rs1571500; hg19: chr1-99386293;