NM_006023.3:c.565+870C>T

Variant names:

• chr10-12235993-C-T
• rs7068966
• NM_006023.3:c.565+870C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006023.3(CDC123):​c.565+870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 152,074 control chromosomes in the GnomAD database, including 15,615 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 0.43 (15615 hom., cov: 33)
• Consequence: CDC123 NM_006023.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351
• Publications: 46 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]

ENSG00000228302 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.519 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC123	NM_006023.3	MANE Select	c.565+870C>T		intron	N/A	NP_006014.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC123	ENST00000281141.9	TSL:1 MANE Select	c.565+870C>T		intron	N/A	ENSP00000281141.4
	CDC123	ENST00000378900.6	TSL:5	c.565+870C>T		intron	N/A	ENSP00000368178.2
	CDC123	ENST00000442050.5	TSL:5	c.469+870C>T		intron	N/A	ENSP00000398724.1

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65601 AN: 151956 Hom.: 15605 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.467

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.432 AC: 65636 AN: 152074 Hom.: 15615 Cov.: 33 AF XY: 0.433 AC XY: 32219 AN XY: 74328

African (AFR) AF: 0.224 AC: 9282 AN: 41496

American (AMR) AF: 0.525 AC: 8004 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1750 AN: 5182

South Asian (SAS) AF: 0.471 AC: 2270 AN: 4820

European-Finnish (FIN) AF: 0.496 AC: 5238 AN: 10556

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35627 AN: 67986

Other (OTH) AF: 0.472 AC: 999 AN: 2116

Alfa AF: 0.489 Hom.: 57151

Bravo AF: 0.426

Asia WGS AF: 0.440 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.5
DANN	Benign	0.85
PhyloP100		0.35
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: rs7068966; hg19: chr10-12277992;