rs12337836

chr9-101314314-C-Achr9-101314314-C-G

Variant summary

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

The NM_207299.2(PLPPR1):c.813+1340C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0568 in 152,254 control chromosomes in the GnomAD database, including 387 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 0.057 (387 hom., cov: 32)
• Consequence: PLPPR1 NM_207299.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

Genes affected

PLPPR1 (HGNC:25993): (phospholipid phosphatase related 1) This gene encodes a member of the plasticity-related gene (PRG) family. Members of the PRG family mediate lipid phosphate phosphatase activity in neurons and are known to be involved in neuronal plasticity. The protein encoded by this gene does not perform its function through enzymatic phospholipid degradation. This gene is strongly expressed in brain. It shows dynamic expression regulation during brain development and neuronal excitation. Alternatively spliced transcript variants encoding the same protein have been observed. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLPPR1	NM_207299.2	c.813+1340C>A		intron_variant		ENST00000374874.8
PLPPR1	NM_017753.3	c.813+1340C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLPPR1	ENST00000374874.8	c.813+1340C>A		intron_variant		1	NM_207299.2	P1
PLPPR1	ENST00000395056.2	c.813+1340C>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.0569 AC: 8650 AN: 152136 Hom.: 387 Cov.: 32

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.0666

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0568 AC: 8647 AN: 152254 Hom.: 387 Cov.: 32 AF XY: 0.0618 AC XY: 4599 AN XY: 74450

Gnomad4 AFR AF: 0.0109

Gnomad4 AMR AF: 0.0431

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.0780

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.0666

Gnomad4 OTH AF: 0.0506

Alfa AF: 0.0624 Hom.: 121

Bravo AF: 0.0465

Asia WGS AF: 0.0780 AC: 272 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	1.9
Dann	Benign	0.67

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: rs12337836; hg19: chr9-104076596;