NM_207299.2:c.-45-54702C>A

Variant names:

• chr9-101130748-C-A
• rs17829436
• NM_207299.2:c.-45-54702C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207299.2(PLPPR1):​c.-45-54702C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,130 control chromosomes in the GnomAD database, including 1,963 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 0.15 (1963 hom., cov: 32)
• Consequence: PLPPR1 NM_207299.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207299.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLPPR1	NM_207299.2	MANE Select	c.-45-54702C>A		intron	N/A	NP_997182.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLPPR1	ENST00000374874.8	TSL:1 MANE Select	c.-45-54702C>A		intron	N/A	ENSP00000364008.3
	PLPPR1	ENST00000883512.1		c.-45-54702C>A		intron	N/A	ENSP00000553571.1
	PLPPR1	ENST00000883511.1		c.-45-54702C>A		intron	N/A	ENSP00000553570.1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22188 AN: 152012 Hom.: 1958 Cov.: 32

Gnomad AFR AF: 0.0537

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0787

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.146 AC: 22198 AN: 152130 Hom.: 1963 Cov.: 32 AF XY: 0.143 AC XY: 10661 AN XY: 74356

African (AFR) AF: 0.0535 AC: 2223 AN: 41530

American (AMR) AF: 0.190 AC: 2905 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3462

East Asian (EAS) AF: 0.0791 AC: 410 AN: 5184

South Asian (SAS) AF: 0.123 AC: 594 AN: 4832

European-Finnish (FIN) AF: 0.145 AC: 1538 AN: 10572

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.197 AC: 13389 AN: 67976

Other (OTH) AF: 0.170 AC: 359 AN: 2112

Alfa AF: 0.166 Hom.: 1310

Bravo AF: 0.145

Asia WGS AF: 0.0960 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.23
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: rs17829436; hg19: chr9-103893030;