rs3814254

Variant names:

• chr13-113457972-C-A
• rs3814254
• NM_001014283.2:c.*57G>T

Your query was ambiguous. Multiple possible variants found:

• chr13-113457972-C-A
• chr13-113457972-C-T

Variant summary

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

The NM_001014283.2(DCUN1D2):​c.*57G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 1,501,582 control chromosomes in the GnomAD database, including 34,776 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 0.27 (6755 hom., cov: 33)
  • Exomes 𝑓: 0.19 (28021 hom.)
• Consequence: DCUN1D2 NM_001014283.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 12 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCUN1D2	NM_001014283.2	c.*57G>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000478244.6	NP_001014305.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCUN1D2	ENST00000478244.6	c.*57G>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_001014283.2	ENSP00000417706.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40857 AN: 151986 Hom.: 6726 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.190 AC: 256872 AN: 1349478 Hom.: 28021 Cov.: 20 AF XY: 0.189 AC XY: 127864 AN XY: 676744

African (AFR) AF: 0.452 AC: 14157 AN: 31298

American (AMR) AF: 0.423 AC: 18830 AN: 44476

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 3294 AN: 25378

East Asian (EAS) AF: 0.225 AC: 8800 AN: 39050

South Asian (SAS) AF: 0.221 AC: 18513 AN: 83948

European-Finnish (FIN) AF: 0.181 AC: 9521 AN: 52724

Middle Eastern (MID) AF: 0.132 AC: 727 AN: 5522

European-Non Finnish (NFE) AF: 0.170 AC: 171875 AN: 1010502

Other (OTH) AF: 0.197 AC: 11155 AN: 56580

GnomAD4 genome AF: 0.269 AC: 40948 AN: 152104 Hom.: 6755 Cov.: 33 AF XY: 0.268 AC XY: 19938 AN XY: 74342

African (AFR) AF: 0.454 AC: 18822 AN: 41472

American (AMR) AF: 0.316 AC: 4830 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3472

East Asian (EAS) AF: 0.230 AC: 1192 AN: 5172

South Asian (SAS) AF: 0.225 AC: 1087 AN: 4828

European-Finnish (FIN) AF: 0.188 AC: 1994 AN: 10592

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11868 AN: 67966

Other (OTH) AF: 0.252 AC: 534 AN: 2116

Alfa AF: 0.210 Hom.: 2967

Bravo AF: 0.287

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.69
PhyloP100		-0.37
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: rs3814254; hg19: chr13-114112287; COSMIC: COSV60260920; COSMIC: COSV60260920;