rs7641401

chr3-182955408-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCUN1D1	NM_020640.4	c.520+5818G>A		intron_variant		ENST00000292782.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCUN1D1	ENST00000292782.9	c.520+5818G>A		intron_variant		1	NM_020640.4	P1
C9orf85P2	ENST00000460975.1	n.303G>A		non_coding_transcript_exon_variant	3/4

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

Gnomad4 AFR exome AF: 0.742

Gnomad4 AMR exome AF: 0.662

Gnomad4 ASJ exome AF: 0.631

Gnomad4 EAS exome AF: 0.262

Gnomad4 SAS exome AF: 0.611

Gnomad4 FIN exome AF: 0.769

Gnomad4 NFE exome AF: 0.764

Gnomad4 OTH exome AF: 0.705

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

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.715

Alfa AF: 0.756 Hom.: 14403

Bravo AF: 0.722

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.8
Dann	Benign	0.80
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

LitVar

Other links and lift over

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