rs11250127
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015458.4(MTMR9):c.972-2223G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,106 control chromosomes in the GnomAD database, including 11,263 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 0.36 ( 11263 hom., cov: 33)
Consequence
MTMR9
NM_015458.4 intron
NM_015458.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.252
Genes affected
MTMR9 (HGNC:14596): (myotubularin related protein 9) This gene encodes a myotubularin-related protein that is atypical to most other members of the myotubularin-related protein family because it has no dual-specificity phosphatase domain. The encoded protein contains a double-helical motif similar to the SET interaction domain, which is thought to have a role in the control of cell proliferation. In mouse, a protein similar to the encoded protein binds with MTMR7, and together they dephosphorylate phosphatidylinositol 3-phosphate and inositol 1,3-bisphosphate. [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=-0.86).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTMR9 | NM_015458.4 | c.972-2223G>A | intron_variant | ENST00000221086.8 | |||
MTMR9 | XM_011543831.3 | c.384-2223G>A | intron_variant | ||||
MTMR9 | XM_017013753.3 | c.972-2165G>A | intron_variant | ||||
MTMR9 | XM_047422125.1 | c.972-2223G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTMR9 | ENST00000221086.8 | c.972-2223G>A | intron_variant | 1 | NM_015458.4 | P1 | |||
MTMR9 | ENST00000530200.1 | c.*718-2223G>A | intron_variant, NMD_transcript_variant | 1 | |||||
MTMR9 | ENST00000526292.1 | c.717-2223G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.363 AC: 55096AN: 151988Hom.: 11262 Cov.: 33
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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: 0.362 AC: 55110AN: 152106Hom.: 11263 Cov.: 33 AF XY: 0.370 AC XY: 27510AN XY: 74344
GnomAD4 genome
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1812
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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