dbSNP rs11597439: CUEDC2:c.-8G>C (chr10-102425196-C-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_024040.3(CUEDC2):c.-8G>C variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 1,609,758 control chromosomes in the GnomAD database, including 92,013 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 0.29 ( 7060 hom., cov: 32)

Exomes 𝑓: 0.34 ( 84953 hom. )

Consequence

CUEDC2
NM_024040.3 splice_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.71

Publications

12 publications found

Variant links:

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]

CUEDC2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CUEDC2	NM_024040.3 link	c.-8G>C		splice_region_variant	Exon 2 of 9	ENST00000369937.5	NP_076945.2	Q9H467
CUEDC2	NM_024040.3 link	c.-8G>C		5_prime_UTR_variant	Exon 2 of 9	ENST00000369937.5	NP_076945.2	Q9H467

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CUEDC2	ENST00000369937.5 link	c.-8G>C	splice_region_variant	Exon 2 of 9	1	NM_024040.3	ENSP00000358953.4	Q9H467
CUEDC2	ENST00000369937.5 link	c.-8G>C	5_prime_UTR_variant	Exon 2 of 9	1	NM_024040.3	ENSP00000358953.4	Q9H467
CUEDC2	ENST00000477994.1 link	n.62G>C	splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 5	2
CUEDC2	ENST00000486762.6 link	n.44-404G>C	intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.291

AC:

44275

AN:

151952

Hom.:

7063

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.387

Gnomad AMR

AF:

0.356

Gnomad ASJ

AF:

0.336

Gnomad EAS

AF:

0.197

Gnomad SAS

AF:

0.442

Gnomad FIN

AF:

0.334

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.330

GnomAD2 exomes

AF:

0.342

AC:

85049

AN:

248508

AF XY:

0.350

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.401

Gnomad ASJ exome

AF:

0.350

Gnomad EAS exome

AF:

0.175

Gnomad FIN exome

AF:

0.339

Gnomad NFE exome

AF:

0.347

Gnomad OTH exome

AF:

0.354

GnomAD4 exome

AF:

0.336

AC:

489767

AN:

1457688

Hom.:

84953

Cov.:

AF XY:

0.340

AC XY:

246816

AN XY:

725372

show subpopulations

African (AFR)

AF:

0.152

AC:

5072

AN:

33424

American (AMR)

AF:

0.393

AC:

17548

AN:

44680

Ashkenazi Jewish (ASJ)

AF:

0.345

AC:

9005

AN:

26112

East Asian (EAS)

AF:

0.210

AC:

8351

AN:

39674

South Asian (SAS)

AF:

0.452

AC:

38924

AN:

86190

European-Finnish (FIN)

AF:

0.340

AC:

18001

AN:

52910

Middle Eastern (MID)

AF:

0.438

AC:

2522

AN:

5760

European-Non Finnish (NFE)

AF:

0.334

AC:

370575

AN:

1108668

Other (OTH)

AF:

0.328

AC:

19769

AN:

60270

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

14700

29400

44100

58800

73500

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11842

23684

35526

47368

59210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.291

AC:

44272

AN:

152070

Hom.:

7060

Cov.:

AF XY:

0.295

AC XY:

21908

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.158

AC:

6542

AN:

41494

American (AMR)

AF:

0.356

AC:

5441

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.336

AC:

1166

AN:

3472

East Asian (EAS)

AF:

0.197

AC:

1016

AN:

5158

South Asian (SAS)

AF:

0.442

AC:

2133

AN:

4822

European-Finnish (FIN)

AF:

0.334

AC:

3534

AN:

10582

Middle Eastern (MID)

AF:

0.401

AC:

118

AN:

294

European-Non Finnish (NFE)

AF:

0.343

AC:

23283

AN:

67946

Other (OTH)

AF:

0.326

AC:

687

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1593

3185

4778

6370

7963

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.275

Hom.:

1399

Bravo

AF:

0.286

Asia WGS

AF:

0.322

AC:

1120

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

1.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=299/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.39

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.39

Position offset: -3

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over