13-113456345-A-G

Position:

• chr13-113456345-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001014283.2(DCUN1D2):​c.*1684T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 398,552 control chromosomes in the GnomAD database, including 35,397 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 0.47 (19658 hom., cov: 33)
  • Exomes 𝑓: 0.35 (15739 hom.)
• Consequence: DCUN1D2 NM_001014283.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

DCUN1D2 (HGNC:20328): (defective in cullin neddylation 1 domain containing 2) Enables cullin family protein binding activity. Involved in positive regulation of protein neddylation. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCUN1D2	NM_001014283.2	c.*1684T>C		3_prime_UTR_variant	7/7	ENST00000478244.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCUN1D2	ENST00000478244.6	c.*1684T>C		3_prime_UTR_variant	7/7	1	NM_001014283.2	P1
DCUN1D2	ENST00000332592.7	c.*1684T>C		3_prime_UTR_variant	5/5	2
DCUN1D2	ENST00000375403.6	c.*2055T>C		3_prime_UTR_variant, NMD_transcript_variant	8/8	2

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71168 AN: 151998 Hom.: 19617 Cov.: 33

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.451

GnomAD4 exome AF: 0.345 AC: 85074 AN: 246436 Hom.: 15739 Cov.: 0 AF XY: 0.342 AC XY: 42679 AN XY: 124902

Gnomad4 AFR exome AF: 0.778

Gnomad4 AMR exome AF: 0.522

Gnomad4 ASJ exome AF: 0.305

Gnomad4 EAS exome AF: 0.358

Gnomad4 SAS exome AF: 0.341

Gnomad4 FIN exome AF: 0.298

Gnomad4 NFE exome AF: 0.320

Gnomad4 OTH exome AF: 0.383

GnomAD4 genome AF: 0.469 AC: 71273 AN: 152116 Hom.: 19658 Cov.: 33 AF XY: 0.462 AC XY: 34376 AN XY: 74372

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.453

Alfa AF: 0.341 Hom.: 12834

Bravo AF: 0.497

Asia WGS AF: 0.425 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs14067; hg19: chr13-114110660;