9-101112137-T-A

Position:

• chr9-101112137-T-A

Variant summary

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

The NM_207299.2(PLPPR1):​c.-45-73313T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,188 control chromosomes in the GnomAD database, including 2,296 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 0.16 (2296 hom., cov: 33)
• Consequence: PLPPR1 NM_207299.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLPPR1	NM_207299.2	c.-45-73313T>A		intron_variant		ENST00000374874.8	NP_997182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLPPR1	ENST00000374874.8	c.-45-73313T>A		intron_variant		1	NM_207299.2	ENSP00000364008.3

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23925 AN: 152072 Hom.: 2291 Cov.: 33

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0905

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.157 AC: 23935 AN: 152188 Hom.: 2296 Cov.: 33 AF XY: 0.154 AC XY: 11492 AN XY: 74396

Gnomad4 AFR AF: 0.0559

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0909

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.181

Alfa AF: 0.188 Hom.: 364

Bravo AF: 0.156

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.27

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: rs17761685; hg19: chr9-103874419;