rs670358

chr11-64824207-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDC42BPG	NM_017525.3	c.*266C>T		3_prime_UTR_variant	37/37	ENST00000342711.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDC42BPG	ENST00000342711.6	c.*266C>T		3_prime_UTR_variant	37/37	1	NM_017525.3	P1

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

Gnomad4 AFR exome AF: 0.0807

Gnomad4 AMR exome AF: 0.318

Gnomad4 ASJ exome AF: 0.0452

Gnomad4 EAS exome AF: 0.369

Gnomad4 SAS exome AF: 0.148

Gnomad4 FIN exome AF: 0.343

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 0.145

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

Gnomad4 AFR AF: 0.0805

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.0447

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.127

Alfa AF: 0.112 Hom.: 1739

Bravo AF: 0.136

Asia WGS AF: 0.288 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	4.7
Dann	Benign	0.69

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: rs670358; hg19: chr11-64591679;