dbSNP rs4859146: DCUN1D1:p.Ala106Ala (chr3-182963952-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_020640.4(DCUN1D1):c.318G>A(p.Ala106Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 1,613,228 control chromosomes in the GnomAD database, including 446,850 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 ( 41047 hom., cov: 32)

Exomes 𝑓: 0.74 ( 405803 hom. )

Consequence

DCUN1D1
NM_020640.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.41

Publications

24 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP7

Synonymous conserved (PhyloP=-2.41 with no splicing effect.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCUN1D1	NM_020640.4 link	c.318G>A	p.Ala106Ala	synonymous_variant	Exon 3 of 7	ENST00000292782.9	NP_065691.2	Q96GG9B4DM76

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCUN1D1	ENST00000292782.9 link	c.318G>A	p.Ala106Ala	synonymous_variant	Exon 3 of 7	1	NM_020640.4	ENSP00000292782.4		Q96GG9

Frequencies

GnomAD3 genomes

AF:

0.728

AC:

110586

AN:

152008

Hom.:

41012

Cov.:

show subpopulations

Gnomad AFR

AF:

0.743

Gnomad AMI

AF:

0.852

Gnomad AMR

AF:

0.683

Gnomad ASJ

AF:

0.631

Gnomad EAS

AF:

0.262

Gnomad SAS

AF:

0.610

Gnomad FIN

AF:

0.772

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.769

Gnomad OTH

AF:

0.717

GnomAD2 exomes

AF:

0.687

AC:

172491

AN:

251252

AF XY:

0.686

show subpopulations

Gnomad AFR exome

AF:

0.738

Gnomad AMR exome

AF:

0.661

Gnomad ASJ exome

AF:

0.634

Gnomad EAS exome

AF:

0.286

Gnomad FIN exome

AF:

0.770

Gnomad NFE exome

AF:

0.759

Gnomad OTH exome

AF:

0.698

GnomAD4 exome

AF:

0.738

AC:

1078653

AN:

1461102

Hom.:

405803

Cov.:

AF XY:

0.735

AC XY:

534010

AN XY:

726910

show subpopulations

African (AFR)

AF:

0.745

AC:

24923

AN:

33472

American (AMR)

AF:

0.667

AC:

29791

AN:

44684

Ashkenazi Jewish (ASJ)

AF:

0.636

AC:

16608

AN:

26116

East Asian (EAS)

AF:

0.229

AC:

9080

AN:

39664

South Asian (SAS)

AF:

0.621

AC:

53538

AN:

86176

European-Finnish (FIN)

AF:

0.770

AC:

41127

AN:

53380

Middle Eastern (MID)

AF:

0.669

AC:

3857

AN:

5766

European-Non Finnish (NFE)

AF:

0.771

AC:

856417

AN:

1111478

Other (OTH)

AF:

0.717

AC:

43312

AN:

60366

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

13496

26992

40487

53983

67479

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.727

AC:

110663

AN:

152126

Hom.:

41047

Cov.:

AF XY:

0.722

AC XY:

53723

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.743

AC:

30822

AN:

41480

American (AMR)

AF:

0.682

AC:

10431

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

2188

AN:

3468

East Asian (EAS)

AF:

0.263

AC:

1357

AN:

5168

South Asian (SAS)

AF:

0.610

AC:

2940

AN:

4818

European-Finnish (FIN)

AF:

0.772

AC:

8165

AN:

10580

Middle Eastern (MID)

AF:

0.680

AC:

200

AN:

294

European-Non Finnish (NFE)

AF:

0.769

AC:

52275

AN:

68006

Other (OTH)

AF:

0.715

AC:

1510

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1530

3060

4589

6119

7649

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.750

Hom.:

22907

Bravo

AF:

0.720

Asia WGS

AF:

0.473

AC:

1649

AN:

3478

EpiCase

AF:

0.760

EpiControl

AF:

0.750

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

5.0

(source)

DANN

Benign

0.57

PhyloP100

-2.4

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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rs4859146

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over