dbSNP rs11089328: DGCR8:c.1606+110A>G (chr22-20092080-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022720.7(DGCR8):c.1606+110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 836,726 control chromosomes in the GnomAD database, including 79,356 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 0.41 ( 13294 hom., cov: 32)

Exomes 𝑓: 0.43 ( 66062 hom. )

Consequence

DGCR8
NM_022720.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.973

Publications

14 publications found

Variant links:

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]

DGCR8 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022720.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DGCR8	NM_022720.7	MANE Select	c.1606+110A>G		intron	N/A	NP_073557.3
	DGCR8	NM_001190326.2		c.1606+110A>G		intron	N/A	NP_001177255.1	Q8WYQ5-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DGCR8	ENST00000351989.8	TSL:1 MANE Select	c.1606+110A>G	intron	N/A	ENSP00000263209.3	Q8WYQ5-1
DGCR8	ENST00000407755.2	TSL:1	c.1606+110A>G	intron	N/A	ENSP00000384726.1	Q8WYQ5-3
DGCR8	ENST00000495826.5	TSL:1	n.2228+110A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.410

AC:

62282

AN:

151930

Hom.:

13282

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.407

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.415

Gnomad EAS

AF:

0.673

Gnomad SAS

AF:

0.550

Gnomad FIN

AF:

0.453

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.398

Gnomad OTH

AF:

0.426

GnomAD4 exome

AF:

0.430

AC:

294104

AN:

684678

Hom.:

66062

AF XY:

0.434

AC XY:

154126

AN XY:

354954

show subpopulations

African (AFR)

AF:

0.316

AC:

5491

AN:

17372

American (AMR)

AF:

0.567

AC:

15829

AN:

27912

Ashkenazi Jewish (ASJ)

AF:

0.413

AC:

7314

AN:

17714

East Asian (EAS)

AF:

0.634

AC:

20343

AN:

32110

South Asian (SAS)

AF:

0.551

AC:

32328

AN:

58624

European-Finnish (FIN)

AF:

0.445

AC:

18736

AN:

42106

Middle Eastern (MID)

AF:

0.313

AC:

1286

AN:

4110

European-Non Finnish (NFE)

AF:

0.395

AC:

178206

AN:

450866

Other (OTH)

AF:

0.430

AC:

14571

AN:

33864

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

8113

16225

24338

32450

40563

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3356

6712

10068

13424

16780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.410

AC:

62335

AN:

152048

Hom.:

13294

Cov.:

AF XY:

0.420

AC XY:

31177

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.336

AC:

13945

AN:

41460

American (AMR)

AF:

0.498

AC:

7617

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.415

AC:

1440

AN:

3468

East Asian (EAS)

AF:

0.673

AC:

3474

AN:

5162

South Asian (SAS)

AF:

0.548

AC:

2640

AN:

4814

European-Finnish (FIN)

AF:

0.453

AC:

4782

AN:

10554

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.398

AC:

27073

AN:

67978

Other (OTH)

AF:

0.427

AC:

901

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1872

3743

5615

7486

9358

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

610

1220

1830

2440

3050

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.407

Hom.:

21657

Bravo

AF:

0.411

Asia WGS

AF:

0.561

AC:

1948

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

(source)

DANN

Benign

0.17

PhyloP100

-0.97

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over