rs1051055

Variant names:

• chr10-12250455-A-G
• rs1051055
• NM_006023.3:c.*118A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-12250455-A-G
• chr10-12250455-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 29 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006023.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC123	NM_006023.3	MANE Select	c.*118A>G		3_prime_UTR	Exon 13 of 13	NP_006014.2	O75794

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC123	ENST00000281141.9	TSL:1 MANE Select	c.*118A>G		3_prime_UTR	Exon 13 of 13	ENSP00000281141.4	O75794
	CDC123	ENST00000932716.1		c.*118A>G		3_prime_UTR	Exon 14 of 14	ENSP00000602775.1
	CDC123	ENST00000932723.1		c.*118A>G		3_prime_UTR	Exon 14 of 14	ENSP00000602782.1

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105774 AN: 151806 Hom.: 36954 Cov.: 31

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

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.: 7 AF XY: 0.678 AC XY: 228055 AN XY: 336544

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

GnomAD4 genome AF: 0.697 AC: 105864 AN: 151924 Hom.: 36989 Cov.: 31 AF XY: 0.699 AC XY: 51891 AN XY: 74238

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
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)

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: rs1051055; hg19: chr10-12292454;