11-64832530-G-T

Variant names:

• chr11-64832530-G-T
• rs494252
• NM_017525.3:c.3006-21C>A

Variant summary

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

The ENST00000342711.6(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 ENST00000342711.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 16 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000342711.6. 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
	CDC42BPG	NM_017525.3	MANE Select	c.3006-21C>A		intron	N/A	NP_059995.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC42BPG	ENST00000342711.6	TSL:1 MANE Select	c.3006-21C>A		intron	N/A	ENSP00000345133.5
	CDC42BPG	ENST00000491280.1	TSL:5	n.-48C>A		upstream_gene	N/A

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

GnomAD2 exomes AF: 0.115 AC: 28871 AN: 250872 AF XY: 0.119

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 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

African (AFR) AF: 0.0242 AC: 810 AN: 33476

American (AMR) AF: 0.0352 AC: 1572 AN: 44710

Ashkenazi Jewish (ASJ) AF: 0.0474 AC: 1237 AN: 26108

East Asian (EAS) AF: 0.139 AC: 5509 AN: 39696

South Asian (SAS) AF: 0.132 AC: 11415 AN: 86252

European-Finnish (FIN) AF: 0.280 AC: 14960 AN: 53350

Middle Eastern (MID) AF: 0.0505 AC: 291 AN: 5768

European-Non Finnish (NFE) AF: 0.113 AC: 126028 AN: 1111884

Other (OTH) AF: 0.113 AC: 6853 AN: 60388

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

African (AFR) AF: 0.0280 AC: 1163 AN: 41536

American (AMR) AF: 0.0577 AC: 883 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3472

East Asian (EAS) AF: 0.190 AC: 984 AN: 5174

South Asian (SAS) AF: 0.137 AC: 663 AN: 4826

European-Finnish (FIN) AF: 0.302 AC: 3197 AN: 10590

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7868 AN: 67986

Other (OTH) AF: 0.0820 AC: 173 AN: 2110

Alfa AF: 0.0990 Hom.: 1593

Bravo AF: 0.0765

Asia WGS AF: 0.174 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	16
DANN	Benign	0.73
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs494252; hg19: chr11-64600002; COSMIC: COSV61346203; COSMIC: COSV61346203;