rs11257600

Variant names:

• chr10-12213658-G-T
• rs11257600
• NM_006023.3:c.238-2082G>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.238-2082G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 151,748 control chromosomes in the GnomAD database, including 5,973 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 0.27 (5973 hom., cov: 32)
• Consequence: CDC123 NM_006023.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 8 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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.238-2082G>T		intron	N/A	NP_006014.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC123	ENST00000281141.9	TSL:1 MANE Select	c.238-2082G>T		intron	N/A	ENSP00000281141.4
	CDC123	ENST00000932716.1		c.358-2082G>T		intron	N/A	ENSP00000602775.1
	CDC123	ENST00000932723.1		c.337-2082G>T		intron	N/A	ENSP00000602782.1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41428 AN: 151634 Hom.: 5972 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.273 AC: 41442 AN: 151748 Hom.: 5973 Cov.: 32 AF XY: 0.275 AC XY: 20398 AN XY: 74158

African (AFR) AF: 0.292 AC: 12055 AN: 41342

American (AMR) AF: 0.256 AC: 3899 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1117 AN: 3462

East Asian (EAS) AF: 0.538 AC: 2777 AN: 5164

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4818

European-Finnish (FIN) AF: 0.314 AC: 3290 AN: 10494

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16411 AN: 67920

Other (OTH) AF: 0.259 AC: 546 AN: 2108

Alfa AF: 0.255 Hom.: 1015

Bravo AF: 0.275

Asia WGS AF: 0.344 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.65
PhyloP100		0.030
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: rs11257600; hg19: chr10-12255657;