rs1409313

Positions:

• chr10-102431844-T-C

Variant summary

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

The NM_024040.3(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 NM_024040.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CUEDC2	NM_024040.3	c.-11+682A>G		intron_variant		ENST00000369937.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUEDC2	ENST00000369937.5	c.-11+682A>G		intron_variant		1	NM_024040.3	P1
CUEDC2	ENST00000477994.1	n.59+682A>G		intron_variant, non_coding_transcript_variant		2
CUEDC2	ENST00000486762.6	n.43+682A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.842

Alfa AF: 0.833 Hom.: 12702

Bravo AF: 0.859

Asia WGS AF: 0.883 AC: 3071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.51
DANN	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409313; hg19: chr10-104191601;