rs10489924

Variant names:

• chr1-98993418-T-C
• rs10489924
• NM_001037317.2:c.237+11017A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001037317.2(PLPPR5):​c.237+11017A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0699 in 152,044 control chromosomes in the GnomAD database, including 507 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 0.070 (507 hom., cov: 32)
• Consequence: PLPPR5 NM_001037317.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 4 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLPPR5	NM_001037317.2	c.237+11017A>G		intron_variant	Intron 1 of 5	ENST00000263177.5	NP_001032394.1
PLPPR5	NM_001010861.3	c.237+11017A>G		intron_variant	Intron 1 of 5		NP_001010861.1
PLPPR5	XM_011540838.4	c.189+11017A>G		intron_variant	Intron 2 of 6		XP_011539140.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLPPR5	ENST00000263177.5	c.237+11017A>G		intron_variant	Intron 1 of 5	1	NM_001037317.2	ENSP00000263177.4

Frequencies

GnomAD3 genomes AF: 0.0700 AC: 10631 AN: 151926 Hom.: 506 Cov.: 32

Gnomad AFR AF: 0.0212

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.00830

Gnomad SAS AF: 0.0641

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0957

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0699 AC: 10633 AN: 152044 Hom.: 507 Cov.: 32 AF XY: 0.0705 AC XY: 5242 AN XY: 74332

African (AFR) AF: 0.0212 AC: 878 AN: 41510

American (AMR) AF: 0.0829 AC: 1264 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3470

East Asian (EAS) AF: 0.00832 AC: 43 AN: 5166

South Asian (SAS) AF: 0.0637 AC: 307 AN: 4818

European-Finnish (FIN) AF: 0.110 AC: 1170 AN: 10594

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0957 AC: 6504 AN: 67934

Other (OTH) AF: 0.0721 AC: 152 AN: 2108

Alfa AF: 0.0875 Hom.: 1016

Bravo AF: 0.0646

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	2.6
DANN	Benign	0.77
PhyloP100		-0.24
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: rs10489924; hg19: chr1-99458974;