dbSNP rs1051055: CDC123:c.*118A>G (chr10-12250455-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_006023.3(CDC123):c.*118A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 771,760 control chromosomes in the GnomAD database, including 179,887 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 0.70 ( 36989 hom., cov: 31)

Exomes 𝑓: 0.68 ( 142898 hom. )

Consequence

CDC123
NM_006023.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.55

Publications

29 publications found

Variant links:

Genes affected

CDC123 (HGNC:16827): (cell division cycle 123) Predicted to be involved in eukaryotic translation initiation factor 2 complex assembly and positive regulation of translational initiation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

CDC123 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.065).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDC123	NM_006023.3 link	c.*118A>G		3_prime_UTR_variant	Exon 13 of 13	ENST00000281141.9	NP_006014.2	O75794
CDC123	XM_005252638.5 link	c.*118A>G		3_prime_UTR_variant	Exon 12 of 12		XP_005252695.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC123	ENST00000281141.9 link	c.*118A>G		3_prime_UTR_variant	Exon 13 of 13	1	NM_006023.3	ENSP00000281141.4		O75794

Frequencies

GnomAD3 genomes

AF:

0.697

AC:

105774

AN:

151806

Hom.:

36954

Cov.:

show subpopulations

Gnomad AFR

AF:

0.744

Gnomad AMI

AF:

0.803

Gnomad AMR

AF:

0.703

Gnomad ASJ

AF:

0.686

Gnomad EAS

AF:

0.619

Gnomad SAS

AF:

0.693

Gnomad FIN

AF:

0.676

Gnomad MID

AF:

0.722

Gnomad NFE

AF:

0.675

Gnomad OTH

AF:

0.709

GnomAD2 exomes

AF:

0.674

AC:

141737

AN:

210310

AF XY:

0.675

show subpopulations

Gnomad AFR exome

AF:

0.725

Gnomad AMR exome

AF:

0.691

Gnomad ASJ exome

AF:

0.692

Gnomad EAS exome

AF:

0.594

Gnomad FIN exome

AF:

0.678

Gnomad NFE exome

AF:

0.666

Gnomad OTH exome

AF:

0.678

GnomAD4 exome

AF:

0.677

AC:

419472

AN:

619836

Hom.:

142898

Cov.:

AF XY:

0.678

AC XY:

228055

AN XY:

336544

show subpopulations

African (AFR)

AF:

0.744

AC:

12784

AN:

17178

American (AMR)

AF:

0.691

AC:

25964

AN:

37566

Ashkenazi Jewish (ASJ)

AF:

0.693

AC:

14212

AN:

20520

East Asian (EAS)

AF:

0.693

AC:

23959

AN:

34592

South Asian (SAS)

AF:

0.695

AC:

46674

AN:

67134

European-Finnish (FIN)

AF:

0.677

AC:

35143

AN:

51874

Middle Eastern (MID)

AF:

0.694

AC:

2847

AN:

4102

European-Non Finnish (NFE)

AF:

0.665

AC:

235741

AN:

354238

Other (OTH)

AF:

0.679

AC:

22148

AN:

32632

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

6277

12554

18831

25108

31385

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1410

2820

4230

5640

7050

<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:

0.697

AC:

105864

AN:

151924

Hom.:

36989

Cov.:

AF XY:

0.699

AC XY:

51891

AN XY:

74238

show subpopulations

African (AFR)

AF:

0.744

AC:

30840

AN:

41438

American (AMR)

AF:

0.703

AC:

10704

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.686

AC:

2379

AN:

3466

East Asian (EAS)

AF:

0.620

AC:

3205

AN:

5166

South Asian (SAS)

AF:

0.692

AC:

3334

AN:

4816

European-Finnish (FIN)

AF:

0.676

AC:

7122

AN:

10538

Middle Eastern (MID)

AF:

0.731

AC:

215

AN:

294

European-Non Finnish (NFE)

AF:

0.675

AC:

45844

AN:

67956

Other (OTH)

AF:

0.706

AC:

1489

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1631

3263

4894

6526

8157

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

818

1636

2454

3272

4090

<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:

0.684

Hom.:

71645

Bravo

AF:

0.702

Asia WGS

AF:

0.690

AC:

2401

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.47

PhyloP100

1.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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