rs1409313

Variant names:

• chr10-102431844-T-C
• rs1409313
• NM_024040.3:c.-11+682A>G

Variant summary

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

The ENST00000369937.5(CUEDC2):​c.-11+682A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,130 control chromosomes in the GnomAD database, including 55,095 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 0.85 (55095 hom., cov: 31)
• Consequence: CUEDC2 ENST00000369937.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 10 publications found

Genes affected

CUEDC2 (HGNC:28352): (CUE domain containing 2) Predicted to enable ubiquitin binding activity. Acts upstream of or within negative regulation of cytokine production involved in inflammatory response and negative regulation of macrophage cytokine production. Located in cytosol; nuclear membrane; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000298413 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000369937.5. 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
	CUEDC2	NM_024040.3	MANE Select	c.-11+682A>G		intron	N/A	NP_076945.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CUEDC2	ENST00000369937.5	TSL:1 MANE Select	c.-11+682A>G		intron	N/A	ENSP00000358953.4
	CUEDC2	ENST00000477994.1	TSL:2	n.59+682A>G		intron	N/A
	CUEDC2	ENST00000486762.6	TSL:3	n.43+682A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129149 AN: 152012 Hom.: 55047 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.850 AC: 129257 AN: 152130 Hom.: 55095 Cov.: 31 AF XY: 0.851 AC XY: 63250 AN XY: 74360

African (AFR) AF: 0.911 AC: 37826 AN: 41506

American (AMR) AF: 0.869 AC: 13297 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2914 AN: 3470

East Asian (EAS) AF: 0.812 AC: 4183 AN: 5152

South Asian (SAS) AF: 0.935 AC: 4512 AN: 4826

European-Finnish (FIN) AF: 0.789 AC: 8348 AN: 10582

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55308 AN: 67982

Other (OTH) AF: 0.842 AC: 1779 AN: 2112

Alfa AF: 0.837 Hom.: 21905

Bravo AF: 0.859

Asia WGS AF: 0.883 AC: 3071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.51
DANN	Benign	0.70
PhyloP100		-1.2
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: rs1409313; hg19: chr10-104191601;