rs2513993

Variant names:

• chr11-103082247-A-G
• rs2513993
• NM_032299.4:c.341+501T>C

Variant summary

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

The NM_032299.4(DCUN1D5):​c.341+501T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,008 control chromosomes in the GnomAD database, including 8,612 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 0.32 (8612 hom., cov: 32)
• Consequence: DCUN1D5 NM_032299.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 1 publications found

Genes affected

DCUN1D5 (HGNC:28409): (defective in cullin neddylation 1 domain containing 5) Enables cullin family protein binding activity. Involved in cellular response to DNA damage stimulus; positive regulation of protein neddylation; and regulation of cell growth. Located in nucleus and spindle. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCUN1D5	NM_032299.4	c.341+501T>C		intron_variant	Intron 4 of 7	ENST00000260247.10	NP_115675.1
DCUN1D5	NM_001318739.2	c.134+501T>C		intron_variant	Intron 4 of 7		NP_001305668.1
DCUN1D5	NM_001318740.2	c.2+1009T>C		intron_variant	Intron 3 of 6		NP_001305669.1
DCUN1D5	NM_001318741.2	c.2+1009T>C		intron_variant	Intron 3 of 6		NP_001305670.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCUN1D5	ENST00000260247.10	c.341+501T>C		intron_variant	Intron 4 of 7	1	NM_032299.4	ENSP00000260247.5

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48422 AN: 151890 Hom.: 8599 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.319 AC: 48467 AN: 152008 Hom.: 8612 Cov.: 32 AF XY: 0.316 AC XY: 23483 AN XY: 74298

African (AFR) AF: 0.487 AC: 20187 AN: 41462

American (AMR) AF: 0.232 AC: 3546 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 942 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1154 AN: 5182

South Asian (SAS) AF: 0.269 AC: 1296 AN: 4826

European-Finnish (FIN) AF: 0.242 AC: 2566 AN: 10598

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17749 AN: 67874

Other (OTH) AF: 0.308 AC: 652 AN: 2116

Alfa AF: 0.290 Hom.: 1476

Bravo AF: 0.325

Asia WGS AF: 0.291 AC: 1008 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.28
PhyloP100		-2.2
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: rs2513993; hg19: chr11-102952976;