rs7641401

Variant names:

• chr3-182955408-C-T
• rs7641401
• NM_020640.4:c.520+5818G>A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609
• Publications: 7 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]

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

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 = 0.763 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

Selected	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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCUN1D1	ENST00000292782.9	TSL:1 MANE Select	c.520+5818G>A		intron	N/A	ENSP00000292782.4
	DCUN1D1	ENST00000632685.1	TSL:1	c.475+5818G>A		intron	N/A	ENSP00000488427.1
	C9orf85P2	ENST00000460975.1	TSL:6	n.303G>A		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110676 AN: 151982 Hom.: 41095 Cov.: 32

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.: 0 AF XY: 0.697 AC XY: 154310 AN XY: 221484

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

GnomAD4 genome AF: 0.728 AC: 110754 AN: 152100 Hom.: 41131 Cov.: 32 AF XY: 0.723 AC XY: 53746 AN XY: 74354

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

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
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)

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: rs7641401; hg19: chr3-182673196; COSMIC: COSV53044605;