11-64830764-G-C

Variant names:

• chr11-64830764-G-C
• rs7940569
• NM_017525.3:c.3305-508C>G

Variant summary

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

The NM_017525.3(CDC42BPG):​c.3305-508C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,010 control chromosomes in the GnomAD database, including 21,757 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 0.51 (21757 hom., cov: 32)
• Consequence: CDC42BPG NM_017525.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDC42BPG	NM_017525.3	c.3305-508C>G		intron_variant	Intron 28 of 36	ENST00000342711.6	NP_059995.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC42BPG	ENST00000342711.6	c.3305-508C>G		intron_variant	Intron 28 of 36	1	NM_017525.3	ENSP00000345133.5
CDC42BPG	ENST00000491280.1	n.273-306C>G		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77977 AN: 151890 Hom.: 21754 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.513 AC: 78007 AN: 152010 Hom.: 21757 Cov.: 32 AF XY: 0.500 AC XY: 37150 AN XY: 74314

African (AFR) AF: 0.390 AC: 16164 AN: 41436

American (AMR) AF: 0.414 AC: 6324 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2345 AN: 3470

East Asian (EAS) AF: 0.0527 AC: 273 AN: 5184

South Asian (SAS) AF: 0.454 AC: 2183 AN: 4812

European-Finnish (FIN) AF: 0.473 AC: 4999 AN: 10562

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43924 AN: 67952

Other (OTH) AF: 0.527 AC: 1116 AN: 2116

Alfa AF: 0.451 Hom.: 1315

Bravo AF: 0.502

Asia WGS AF: 0.239 AC: 835 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		-0.19
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: rs7940569; hg19: chr11-64598236;