13-113456345-A-G

Variant names:

• chr13-113456345-A-G
• rs14067
• NM_001014283.2:c.*1684T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001014283.2. 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
	DCUN1D2	NM_001014283.2	MANE Select	c.*1684T>C		3_prime_UTR	Exon 7 of 7	NP_001014305.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCUN1D2	ENST00000478244.6	TSL:1 MANE Select	c.*1684T>C		3_prime_UTR	Exon 7 of 7	ENSP00000417706.1
	DCUN1D2	ENST00000375403.6	TSL:2	n.*2055T>C		non_coding_transcript_exon	Exon 8 of 8	ENSP00000364552.2
	DCUN1D2	ENST00000332592.7	TSL:2	c.*1684T>C		3_prime_UTR	Exon 5 of 5	ENSP00000330629.3

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

African (AFR) AF: 0.778 AC: 5586 AN: 7184

American (AMR) AF: 0.522 AC: 3877 AN: 7434

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 2817 AN: 9240

East Asian (EAS) AF: 0.358 AC: 8201 AN: 22896

South Asian (SAS) AF: 0.341 AC: 1033 AN: 3032

European-Finnish (FIN) AF: 0.298 AC: 6214 AN: 20832

Middle Eastern (MID) AF: 0.376 AC: 486 AN: 1294

European-Non Finnish (NFE) AF: 0.320 AC: 50583 AN: 158142

Other (OTH) AF: 0.383 AC: 6277 AN: 16382

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

African (AFR) AF: 0.775 AC: 32174 AN: 41508

American (AMR) AF: 0.480 AC: 7341 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2209 AN: 5164

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4820

European-Finnish (FIN) AF: 0.297 AC: 3143 AN: 10588

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22139 AN: 67964

Other (OTH) AF: 0.453 AC: 956 AN: 2112

Alfa AF: 0.359 Hom.: 18612

Bravo AF: 0.497

Asia WGS AF: 0.425 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.50
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs14067; hg19: chr13-114110660;