chr2-44218542-GTTTTA-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_002706.6(PPM1B):c.1134+14_1134+18del variant causes a splice donor region, intron change. The variant allele was found at a frequency of 0.00204 in 1,565,766 control chromosomes in the GnomAD database, including 52 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 28 hom., cov: 32)
Exomes 𝑓: 0.0010 ( 24 hom. )
Consequence
PPM1B
NM_002706.6 splice_donor_region, intron
NM_002706.6 splice_donor_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.68
Genes affected
PPM1B (HGNC:9276): (protein phosphatase, Mg2+/Mn2+ dependent 1B) The protein encoded by this gene is a member of the PP2C family of Ser/Thr protein phosphatases. PP2C family members are known to be negative regulators of cell stress response pathways. This phosphatase has been shown to dephosphorylate cyclin-dependent kinases (CDKs), and thus may be involved in cell cycle control. Overexpression of this phosphatase is reported to cause cell-growth arrest or cell death. Alternative splicing results in multiple transcript variants encoding different isoforms. Additional transcript variants have been described, but currently do not represent full-length sequences. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 2-44218542-GTTTTA-G is Benign according to our data. Variant chr2-44218542-GTTTTA-G is described in ClinVar as [Benign]. Clinvar id is 788956.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0114 (1728/152062) while in subpopulation AFR AF= 0.0397 (1645/41474). AF 95% confidence interval is 0.0381. There are 28 homozygotes in gnomad4. There are 837 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 28 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPM1B | NM_002706.6 | c.1134+14_1134+18del | splice_donor_region_variant, intron_variant | ENST00000282412.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPM1B | ENST00000282412.9 | c.1134+14_1134+18del | splice_donor_region_variant, intron_variant | 1 | NM_002706.6 |
Frequencies
GnomAD3 genomes AF: 0.0113 AC: 1723AN: 151944Hom.: 27 Cov.: 32
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GnomAD3 exomes AF: 0.00297 AC: 670AN: 225626Hom.: 12 AF XY: 0.00222 AC XY: 271AN XY: 122334
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GnomAD4 exome AF: 0.00104 AC: 1467AN: 1413704Hom.: 24 AF XY: 0.000906 AC XY: 638AN XY: 704388
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GnomAD4 genome AF: 0.0114 AC: 1728AN: 152062Hom.: 28 Cov.: 32 AF XY: 0.0113 AC XY: 837AN XY: 74350
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 25, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at