rs17761685

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.494
Variant links:
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]

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ACMG classification

Classification made for transcript

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
PLPPR1NM_207299.2 linkuse as main transcriptc.-45-73313T>A intron_variant ENST00000374874.8 NP_997182.1 Q8TBJ4A0A024R154

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PLPPR1ENST00000374874.8 linkuse as main transcriptc.-45-73313T>A intron_variant 1 NM_207299.2 ENSP00000364008.3 Q8TBJ4

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17761685; hg19: chr9-103874419; API