rs3757
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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.*1700G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 204,996 control chromosomes in the GnomAD database, including 5,275 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 0.21 ( 3545 hom., cov: 31)
Exomes 𝑓: 0.22 ( 1730 hom. )
Consequence
DGCR8
NM_022720.7 3_prime_UTR
NM_022720.7 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.262
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=-0.8).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGCR8 | NM_022720.7 | c.*1700G>A | 3_prime_UTR_variant | 14/14 | ENST00000351989.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGCR8 | ENST00000351989.8 | c.*1700G>A | 3_prime_UTR_variant | 14/14 | 1 | NM_022720.7 | P1 | ||
ENST00000412713.1 | n.68C>T | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.208 AC: 31333AN: 150656Hom.: 3545 Cov.: 31
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GnomAD4 exome AF: 0.223 AC: 12070AN: 54224Hom.: 1730 Cov.: 0 AF XY: 0.224 AC XY: 6070AN XY: 27090
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GnomAD4 genome ? AF: 0.208 AC: 31341AN: 150772Hom.: 3545 Cov.: 31 AF XY: 0.209 AC XY: 15374AN XY: 73606
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ClinVar
Not reported inComputational scores
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Name
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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