rs1249935
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020700.2(PPM1H):c.245+9972G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,244 control chromosomes in the GnomAD database, including 61,643 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 0.90 ( 61643 hom., cov: 33)
Consequence
PPM1H
NM_020700.2 intron
NM_020700.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.68
Genes affected
PPM1H (HGNC:18583): (protein phosphatase, Mg2+/Mn2+ dependent 1H) Enables identical protein binding activity and phosphoprotein phosphatase activity. Predicted to be involved in protein dephosphorylation. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.98).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPM1H | NM_020700.2 | c.245+9972G>T | intron_variant | ENST00000228705.7 | |||
PPM1H | XM_011538578.3 | c.131+9403G>T | intron_variant | ||||
PPM1H | XM_017019676.3 | c.245+9972G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPM1H | ENST00000228705.7 | c.245+9972G>T | intron_variant | 1 | NM_020700.2 | P1 | |||
PPM1H | ENST00000548414.5 | n.126+9403G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.898 AC: 136534AN: 152126Hom.: 61617 Cov.: 33
GnomAD3 genomes
?
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136534
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152126
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.897 AC: 136609AN: 152244Hom.: 61643 Cov.: 33 AF XY: 0.896 AC XY: 66693AN XY: 74436
GnomAD4 genome
?
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136609
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152244
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33
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66693
AN XY:
74436
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3351
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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