rs2073778
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022720.7(DGCR8):c.721-110C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,396,062 control chromosomes in the GnomAD database, including 20,149 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 0.13 ( 2225 hom., cov: 32)
Exomes 𝑓: 0.15 ( 17924 hom. )
Consequence
DGCR8
NM_022720.7 intron
NM_022720.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.365
Genes affected
DGCR8 (HGNC:2847): (DGCR8 microprocessor complex subunit) This gene encodes a subunit of the microprocessor complex which mediates the biogenesis of microRNAs from the primary microRNA transcript. The encoded protein is a double-stranded RNA binding protein that functions as the non-catalytic subunit of the microprocessor complex. This protein is required for binding the double-stranded RNA substrate and facilitates cleavage of the RNA by the ribonuclease III protein, Drosha. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2010]
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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=-0.56).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGCR8 | NM_022720.7 | c.721-110C>T | intron_variant | ENST00000351989.8 | |||
DGCR8 | NM_001190326.2 | c.721-110C>T | intron_variant | ||||
DGCR8 | XM_047441418.1 | c.721-110C>T | intron_variant | ||||
DGCR8 | XM_047441419.1 | c.721-110C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGCR8 | ENST00000351989.8 | c.721-110C>T | intron_variant | 1 | NM_022720.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.130 AC: 19806AN: 152110Hom.: 2219 Cov.: 32
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GnomAD4 exome AF: 0.147 AC: 182789AN: 1243834Hom.: 17924 Cov.: 18 AF XY: 0.149 AC XY: 91702AN XY: 614734
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GnomAD4 genome ? AF: 0.130 AC: 19821AN: 152228Hom.: 2225 Cov.: 32 AF XY: 0.139 AC XY: 10352AN XY: 74424
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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