rs1571500
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001037317.2(PLPPR5):c.798+1145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,182 control chromosomes in the GnomAD database, including 1,081 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 0.10 ( 1081 hom., cov: 31)
Consequence
PLPPR5
NM_001037317.2 intron
NM_001037317.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.87
Genes affected
PLPPR5 (HGNC:31703): (phospholipid phosphatase related 5) The protein encoded by this gene is a type 2 member of the phosphatidic acid phosphatase (PAP) family. All type 2 members of this protein family contain 6 transmembrane regions, and a consensus N-glycosylation site. PAPs convert phosphatidic acid to diacylglycerol, and function in de novo synthesis of glycerolipids as well as in receptor-activated signal transduction mediated by phospholipase D. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [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=-0.83).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLPPR5 | NM_001037317.2 | c.798+1145A>G | intron_variant | ENST00000263177.5 | |||
PLPPR5 | NM_001010861.3 | c.798+1145A>G | intron_variant | ||||
PLPPR5 | XM_011540838.4 | c.750+1145A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLPPR5 | ENST00000263177.5 | c.798+1145A>G | intron_variant | 1 | NM_001037317.2 | P4 | |||
PLPPR5 | ENST00000370188.7 | c.798+1145A>G | intron_variant | 1 | A1 | ||||
PLPPR5 | ENST00000672681.1 | c.798+1145A>G | intron_variant | ||||||
PLPPR5 | ENST00000696571.1 | c.633+1145A>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.103 AC: 15639AN: 152064Hom.: 1077 Cov.: 31
GnomAD3 genomes
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31
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GnomAD4 genome ? AF: 0.103 AC: 15656AN: 152182Hom.: 1081 Cov.: 31 AF XY: 0.107 AC XY: 7929AN XY: 74392
GnomAD4 genome
?
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709
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at