rs1571500

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0353 AC: 1467 AN: 41576

American (AMR) AF: 0.188 AC: 2868 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1041 AN: 5178

South Asian (SAS) AF: 0.225 AC: 1084 AN: 4818

European-Finnish (FIN) AF: 0.116 AC: 1224 AN: 10558

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7216 AN: 68002

Other (OTH) AF: 0.114 AC: 240 AN: 2112

Alfa AF: 0.109 Hom.: 1201

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
PhyloP100		1.9
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: rs1571500; hg19: chr1-99386293;