chr11-64824207-G-A

Variant names:

• chr11-64824207-G-A
• rs670358
• NM_017525.3:c.*266C>T

Variant summary

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

The NM_017525.3(CDC42BPG):​c.*266C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 535,706 control chromosomes in the GnomAD database, including 8,996 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 0.14 (2431 hom., cov: 31)
  • Exomes 𝑓: 0.15 (6565 hom.)
• Consequence: CDC42BPG NM_017525.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.724
• Publications: 13 publications found

Genes affected

CDC42BPG (HGNC:29829): (CDC42 binding protein kinase gamma) Enables ATP binding activity; magnesium ion binding activity; and protein serine/threonine kinase activity. Involved in protein phosphorylation. Located in cell leading edge; centriolar satellite; and cytosol. [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=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017525.3. 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
	CDC42BPG	NM_017525.3	MANE Select	c.*266C>T		3_prime_UTR	Exon 37 of 37	NP_059995.2	Q6DT37

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC42BPG	ENST00000342711.6	TSL:1 MANE Select	c.*266C>T		3_prime_UTR	Exon 37 of 37	ENSP00000345133.5	Q6DT37
	CDC42BPG	ENST00000939060.1		c.*266C>T		3_prime_UTR	Exon 37 of 37	ENSP00000609119.1
	CDC42BPG	ENST00000904237.1		c.*266C>T		3_prime_UTR	Exon 37 of 37	ENSP00000574296.1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22025 AN: 151892 Hom.: 2428 Cov.: 31

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.125

GnomAD4 exome AF: 0.153 AC: 58870 AN: 383696 Hom.: 6565 Cov.: 0 AF XY: 0.151 AC XY: 30789 AN XY: 204052

African (AFR) AF: 0.0807 AC: 860 AN: 10660

American (AMR) AF: 0.318 AC: 5211 AN: 16382

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 512 AN: 11322

East Asian (EAS) AF: 0.369 AC: 9378 AN: 25384

South Asian (SAS) AF: 0.148 AC: 6656 AN: 45096

European-Finnish (FIN) AF: 0.343 AC: 9028 AN: 26356

Middle Eastern (MID) AF: 0.0671 AC: 111 AN: 1654

European-Non Finnish (NFE) AF: 0.107 AC: 23990 AN: 225244

Other (OTH) AF: 0.145 AC: 3124 AN: 21598

GnomAD4 genome AF: 0.145 AC: 22035 AN: 152010 Hom.: 2431 Cov.: 31 AF XY: 0.159 AC XY: 11834 AN XY: 74276

African (AFR) AF: 0.0805 AC: 3338 AN: 41474

American (AMR) AF: 0.254 AC: 3869 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0447 AC: 155 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2216 AN: 5150

South Asian (SAS) AF: 0.159 AC: 767 AN: 4812

European-Finnish (FIN) AF: 0.365 AC: 3847 AN: 10552

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7382 AN: 67974

Other (OTH) AF: 0.127 AC: 268 AN: 2114

Alfa AF: 0.117 Hom.: 2751

Bravo AF: 0.136

Asia WGS AF: 0.288 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	4.7
DANN	Benign	0.69
PhyloP100		0.72
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: rs670358; hg19: chr11-64591679;