11-64832530-G-T

Position:

• chr11-64832530-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017525.3(CDC42BPG):​c.3006-21C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,613,830 control chromosomes in the GnomAD database, including 12,338 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 0.10 (1183 hom., cov: 33)
  • Exomes 𝑓: 0.12 (11155 hom.)
• Consequence: CDC42BPG NM_017525.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDC42BPG	NM_017525.3	c.3006-21C>A		intron_variant		ENST00000342711.6	NP_059995.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDC42BPG	ENST00000342711.6	c.3006-21C>A		intron_variant		1	NM_017525.3	ENSP00000345133	P1
CDC42BPG	ENST00000491280.1			upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15294 AN: 152080 Hom.: 1182 Cov.: 33

Gnomad AFR AF: 0.0280

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0790

GnomAD3 exomes AF: 0.115 AC: 28871 AN: 250872 Hom.: 2288 AF XY: 0.119 AC XY: 16139 AN XY: 135582

Gnomad AFR exome AF: 0.0261

Gnomad AMR exome AF: 0.0349

Gnomad ASJ exome AF: 0.0469

Gnomad EAS exome AF: 0.175

Gnomad SAS exome AF: 0.130

Gnomad FIN exome AF: 0.289

Gnomad NFE exome AF: 0.112

Gnomad OTH exome AF: 0.110

GnomAD4 exome AF: 0.115 AC: 168675 AN: 1461632 Hom.: 11155 Cov.: 34 AF XY: 0.116 AC XY: 84236 AN XY: 727114

Gnomad4 AFR exome AF: 0.0242

Gnomad4 AMR exome AF: 0.0352

Gnomad4 ASJ exome AF: 0.0474

Gnomad4 EAS exome AF: 0.139

Gnomad4 SAS exome AF: 0.132

Gnomad4 FIN exome AF: 0.280

Gnomad4 NFE exome AF: 0.113

Gnomad4 OTH exome AF: 0.113

GnomAD4 genome AF: 0.101 AC: 15298 AN: 152198 Hom.: 1183 Cov.: 33 AF XY: 0.108 AC XY: 8066 AN XY: 74406

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.0577

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0820

Alfa AF: 0.100 Hom.: 1173

Bravo AF: 0.0765

Asia WGS AF: 0.174 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	16
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs494252; hg19: chr11-64600002; COSMIC: COSV61346203; COSMIC: COSV61346203;