rs1051055

Positions:

• chr10-12250455-A-G

Variant summary

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

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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/exons	MANE	UniProt
CDC123	NM_006023.3	c.*118A>G		3_prime_UTR_variant	13/13	ENST00000281141.9
CDC123	XM_005252638.5	c.*118A>G		3_prime_UTR_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDC123	ENST00000281141.9	c.*118A>G		3_prime_UTR_variant	13/13	1	NM_006023.3	P1
CDC123	ENST00000440613.1	c.*118A>G		3_prime_UTR_variant	6/6	5
CDC123	ENST00000498747.1	n.816A>G		non_coding_transcript_exon_variant	9/9	3

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

GnomAD3 exomes AF: 0.674 AC: 141737 AN: 210310 Hom.: 47697 AF XY: 0.675 AC XY: 77357 AN XY: 114664

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 SAS exome AF: 0.697

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

Gnomad4 AFR exome AF: 0.744

Gnomad4 AMR exome AF: 0.691

Gnomad4 ASJ exome AF: 0.693

Gnomad4 EAS exome AF: 0.693

Gnomad4 SAS exome AF: 0.695

Gnomad4 FIN exome AF: 0.677

Gnomad4 NFE exome AF: 0.665

Gnomad4 OTH exome AF: 0.679

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

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.706

Alfa AF: 0.682 Hom.: 58591

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	11
DANN	Benign	0.47
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs1051055; hg19: chr10-12292454;