chr3-182946759-G-A

Variant names:

• chr3-182946759-G-A
• rs4859259
• NM_020640.4:c.700+479C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020640.4(DCUN1D1):​c.700+479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,818 control chromosomes in the GnomAD database, including 28,577 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 0.55 (28577 hom., cov: 30)
• Consequence: DCUN1D1 NM_020640.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 9 publications found

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]

ACMG classification

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 = 0.764 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCUN1D1	NM_020640.4	MANE Select	c.700+479C>T		intron	N/A	NP_065691.2
	DCUN1D1	NM_001308101.2		c.655+479C>T		intron	N/A	NP_001295030.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCUN1D1	ENST00000292782.9	TSL:1 MANE Select	c.700+479C>T		intron	N/A	ENSP00000292782.4
	DCUN1D1	ENST00000632685.1	TSL:1	c.655+479C>T		intron	N/A	ENSP00000488427.1
	DCUN1D1	ENST00000925548.1		c.700+479C>T		intron	N/A	ENSP00000595607.1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83478 AN: 151700 Hom.: 28591 Cov.: 30

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.566

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.550 AC: 83438 AN: 151818 Hom.: 28577 Cov.: 30 AF XY: 0.547 AC XY: 40574 AN XY: 74234

African (AFR) AF: 0.146 AC: 6027 AN: 41378

American (AMR) AF: 0.613 AC: 9335 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1957 AN: 3468

East Asian (EAS) AF: 0.232 AC: 1198 AN: 5162

South Asian (SAS) AF: 0.564 AC: 2711 AN: 4810

European-Finnish (FIN) AF: 0.749 AC: 7889 AN: 10536

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.769 AC: 52239 AN: 67922

Other (OTH) AF: 0.560 AC: 1180 AN: 2108

Alfa AF: 0.687 Hom.: 132719

Bravo AF: 0.521

Asia WGS AF: 0.375 AC: 1307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.39
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4859259; hg19: chr3-182664547;