NM_032299.4:c.341+6012A>G

Variant names:

• chr11-103076736-T-C
• rs7947821
• NM_032299.4:c.341+6012A>G

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+6012A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0332 in 152,304 control chromosomes in the GnomAD database, including 286 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 0.033 (286 hom., cov: 32)
• Consequence: DCUN1D5 NM_032299.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 3 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]

ENSG00000303541 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCUN1D5	NM_032299.4	c.341+6012A>G		intron_variant	Intron 4 of 7	ENST00000260247.10	NP_115675.1
DCUN1D5	NM_001318739.2	c.134+6012A>G		intron_variant	Intron 4 of 7		NP_001305668.1
DCUN1D5	NM_001318740.2	c.2+6520A>G		intron_variant	Intron 3 of 6		NP_001305669.1
DCUN1D5	NM_001318741.2	c.2+6520A>G		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+6012A>G		intron_variant	Intron 4 of 7	1	NM_032299.4	ENSP00000260247.5

Frequencies

GnomAD3 genomes AF: 0.0333 AC: 5062 AN: 152186 Hom.: 286 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0120

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000382

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0332 AC: 5063 AN: 152304 Hom.: 286 Cov.: 32 AF XY: 0.0316 AC XY: 2355 AN XY: 74472

African (AFR) AF: 0.116 AC: 4802 AN: 41542

American (AMR) AF: 0.0119 AC: 182 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000382 AC: 26 AN: 68034

Other (OTH) AF: 0.0241 AC: 51 AN: 2114

Alfa AF: 0.0250 Hom.: 60

Bravo AF: 0.0383

Asia WGS AF: 0.00577 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.74
PhyloP100		-0.046
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: rs7947821; hg19: chr11-102947465;