rs10898966
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000328257.13(PPME1):c.1010-1895C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,214 control chromosomes in the GnomAD database, including 2,591 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 0.18 ( 2591 hom., cov: 32)
Exomes 𝑓: 0.25 ( 0 hom. )
Consequence
PPME1
ENST00000328257.13 intron
ENST00000328257.13 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.301
Genes affected
PPME1 (HGNC:30178): (protein phosphatase methylesterase 1) This gene encodes a protein phosphatase methylesterase localized to the nucleus. The encoded protein acts on the protein phosphatase-2A catalytic subunit and supports the ERK pathway through dephosphorylation of regulatory proteins. It plays a role in malignant glioma progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2012]
P4HA3 (HGNC:30135): (prolyl 4-hydroxylase subunit alpha 3) This gene encodes a component of prolyl 4-hydroxylase, a key enzyme in collagen synthesis composed of two identical alpha subunits and two beta subunits. The encoded protein is one of several different types of alpha subunits and provides the major part of the catalytic site of the active enzyme. In collagen and related proteins, prolyl 4-hydroxylase catalyzes the formation of 4-hydroxyproline that is essential to the proper three-dimensional folding of newly synthesized procollagen chains. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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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=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPME1 | NM_016147.3 | c.1010-1895C>T | intron_variant | ENST00000328257.13 | NP_057231.1 | |||
PPME1 | NM_001271593.2 | c.1052-1895C>T | intron_variant | NP_001258522.1 | ||||
PPME1 | XM_047427116.1 | c.1010-1895C>T | intron_variant | XP_047283072.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPME1 | ENST00000328257.13 | c.1010-1895C>T | intron_variant | 1 | NM_016147.3 | ENSP00000329867 | P1 |
Frequencies
GnomAD3 genomes AF: 0.177 AC: 26926AN: 152092Hom.: 2592 Cov.: 32
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GnomAD4 exome AF: 0.250 AC: 1AN: 4Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1AN XY: 4
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GnomAD4 genome AF: 0.177 AC: 26935AN: 152210Hom.: 2591 Cov.: 32 AF XY: 0.184 AC XY: 13682AN XY: 74414
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at