rs12337836

Variant names:

• chr9-101314314-C-A
• rs12337836
• NM_207299.2:c.813+1340C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-101314314-C-A
• chr9-101314314-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PLPPR1	NM_207299.2	c.813+1340C>A		intron_variant	Intron 6 of 7	ENST00000374874.8	NP_997182.1
PLPPR1	NM_017753.3	c.813+1340C>A		intron_variant	Intron 6 of 7		NP_060223.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLPPR1	ENST00000374874.8	c.813+1340C>A		intron_variant	Intron 6 of 7	1	NM_207299.2	ENSP00000364008.3
PLPPR1	ENST00000395056.2	c.813+1340C>A		intron_variant	Intron 6 of 7	1		ENSP00000378496.1

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

African (AFR) AF: 0.0109 AC: 451 AN: 41556

American (AMR) AF: 0.0431 AC: 659 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3472

East Asian (EAS) AF: 0.116 AC: 598 AN: 5176

South Asian (SAS) AF: 0.0780 AC: 376 AN: 4818

European-Finnish (FIN) AF: 0.164 AC: 1740 AN: 10598

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.0666 AC: 4531 AN: 68022

Other (OTH) AF: 0.0506 AC: 107 AN: 2114

Alfa AF: 0.0534 Hom.: 140

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
PhyloP100		-0.39
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: rs12337836; hg19: chr9-104076596;