dbSNP rs7641401: DCUN1D1:c.520+5818G>A (chr3-182955408-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_020640.4(DCUN1D1):c.520+5818G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 541,226 control chromosomes in the GnomAD database, including 139,799 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 0.73 ( 41131 hom., cov: 32)

Exomes 𝑓: 0.70 ( 98668 hom. )

Consequence

DCUN1D1
NM_020640.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.609

Publications

7 publications found

Variant links:

Genes affected

DCUN1D1 (HGNC:18184): (defective in cullin neddylation 1 domain containing 1) Enables cullin family protein binding activity. Involved in positive regulation of protein neddylation and regulation of protein ubiquitination. Located in cytosol and nucleoplasm. Part of ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

DCUN1D1 links:

C9orf85P2 (HGNC:56318): (C9orf85 pseudogene 2)

C9orf85P2 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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020640.4. 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
	DCUN1D1	NM_020640.4	MANE Select	c.520+5818G>A		intron	N/A	NP_065691.2
	DCUN1D1	NM_001308101.2		c.475+5818G>A		intron	N/A	NP_001295030.1	C9JVE2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DCUN1D1	ENST00000292782.9	TSL:1 MANE Select	c.520+5818G>A	intron	N/A	ENSP00000292782.4	Q96GG9
DCUN1D1	ENST00000632685.1	TSL:1	c.475+5818G>A	intron	N/A	ENSP00000488427.1	C9JVE2
DCUN1D1	ENST00000925548.1		c.520+5818G>A	intron	N/A	ENSP00000595607.1

Frequencies

GnomAD3 genomes

AF:

0.728

AC:

110676

AN:

151982

Hom.:

41095

Cov.:

show subpopulations

Gnomad AFR

AF:

0.747

Gnomad AMI

AF:

0.850

Gnomad AMR

AF:

0.683

Gnomad ASJ

AF:

0.631

Gnomad EAS

AF:

0.262

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.772

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.768

Gnomad OTH

AF:

0.718

GnomAD4 exome

AF:

0.703

AC:

273404

AN:

389126

Hom.:

98668

Cov.:

AF XY:

0.697

AC XY:

154310

AN XY:

221484

show subpopulations

African (AFR)

AF:

0.742

AC:

7652

AN:

10312

American (AMR)

AF:

0.662

AC:

23880

AN:

36086

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

7633

AN:

12090

East Asian (EAS)

AF:

0.262

AC:

3749

AN:

14334

South Asian (SAS)

AF:

0.611

AC:

41003

AN:

67144

European-Finnish (FIN)

AF:

0.769

AC:

24691

AN:

32098

Middle Eastern (MID)

AF:

0.701

AC:

1269

AN:

1810

European-Non Finnish (NFE)

AF:

0.764

AC:

151361

AN:

198000

Other (OTH)

AF:

0.705

AC:

12166

AN:

17252

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.543

Heterozygous variant carriers

3700

7399

11099

14798

18498

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

846

1692

2538

3384

4230

<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:

0.728

AC:

110754

AN:

152100

Hom.:

41131

Cov.:

AF XY:

0.723

AC XY:

53746

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.748

AC:

31006

AN:

41474

American (AMR)

AF:

0.682

AC:

10440

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

2190

AN:

3470

East Asian (EAS)

AF:

0.262

AC:

1356

AN:

5166

South Asian (SAS)

AF:

0.597

AC:

2873

AN:

4816

European-Finnish (FIN)

AF:

0.772

AC:

8153

AN:

10564

Middle Eastern (MID)

AF:

0.677

AC:

199

AN:

294

European-Non Finnish (NFE)

AF:

0.768

AC:

52256

AN:

68000

Other (OTH)

AF:

0.715

AC:

1506

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1480

2960

4440

5920

7400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

834

1668

2502

3336

4170

<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:

0.756

Hom.:

14403

Bravo

AF:

0.722

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.8

(source)

DANN

Benign

0.80

PhyloP100

0.61

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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