rs17409275
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001382508.1(DROSHA):c.1290+968G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,738 control chromosomes in the GnomAD database, including 10,152 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 0.34 ( 10152 hom., cov: 32)
Consequence
DROSHA
NM_001382508.1 intron
NM_001382508.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.12
Genes affected
DROSHA (HGNC:17904): (drosha ribonuclease III) This gene encodes a ribonuclease (RNase) III double-stranded RNA-specific ribonuclease and subunit of the microprocessor protein complex, which catalyzes the initial processing step of microRNA (miRNA) synthesis. The encoded protein cleaves the stem loop structure from the primary microRNA (pri-miRNA) in the nucleus, yielding the precursor miRNA (pre-miRNA), which is then exported to the cytoplasm for further processing. In a human cell line lacking a functional copy of this gene, canonical miRNA synthesis is reduced. Somatic mutations in this gene have been observed in human patients with kidney cancer. [provided by RefSeq, Sep 2016]
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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=-0.97).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DROSHA | NM_001382508.1 | c.1290+968G>A | intron_variant | ENST00000344624.8 | |||
DROSHA | NM_001100412.2 | c.1179+968G>A | intron_variant | ||||
DROSHA | NM_013235.5 | c.1290+968G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DROSHA | ENST00000344624.8 | c.1290+968G>A | intron_variant | 5 | NM_001382508.1 | P4 | |||
DROSHA | ENST00000511367.6 | c.1290+968G>A | intron_variant | 1 | P4 | ||||
DROSHA | ENST00000512076.1 | c.574+968G>A | intron_variant | 1 | |||||
DROSHA | ENST00000513349.5 | c.1179+968G>A | intron_variant | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.339 AC: 51439AN: 151620Hom.: 10156 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.339 AC: 51433AN: 151738Hom.: 10152 Cov.: 32 AF XY: 0.337 AC XY: 24982AN XY: 74122
GnomAD4 genome
?
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51433
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24982
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74122
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740
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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