11-64829667-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_017525.3(CDC42BPG):c.3771G>A(p.Pro1257=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00492 in 1,611,652 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0032 (1 hom., cov: 34)
  • Exomes 𝑓: 0.0051 (28 hom.)
• Consequence: CDC42BPG NM_017525.3 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.243

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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 11-64829667-C-T is Benign according to our data. Variant chr11-64829667-C-T is described in ClinVar as [Benign]. Clinvar id is 717710.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.243 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDC42BPG	NM_017525.3	c.3771G>A	p.Pro1257=	synonymous_variant	30/37	ENST00000342711.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDC42BPG	ENST00000342711.6	c.3771G>A	p.Pro1257=	synonymous_variant	30/37	1	NM_017525.3	P1

Frequencies

GnomAD3 genomes AF: 0.00320 AC: 488 AN: 152272 Hom.: 1 Cov.: 34

Gnomad AFR AF: 0.00133

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000915

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.000941

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00497

Gnomad OTH AF: 0.00382

GnomAD3 exomes AF: 0.00399 AC: 954 AN: 239016 Hom.: 2 AF XY: 0.00466 AC XY: 612 AN XY: 131316

Gnomad AFR exome AF: 0.00118

Gnomad AMR exome AF: 0.000382

Gnomad ASJ exome AF: 0.00133

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0105

Gnomad FIN exome AF: 0.00103

Gnomad NFE exome AF: 0.00517

Gnomad OTH exome AF: 0.00343

GnomAD4 exome AF: 0.00510 AC: 7440 AN: 1459262 Hom.: 28 Cov.: 77 AF XY: 0.00529 AC XY: 3838 AN XY: 725944

Gnomad4 AFR exome AF: 0.00108

Gnomad4 AMR exome AF: 0.000382

Gnomad4 ASJ exome AF: 0.00107

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0109

Gnomad4 FIN exome AF: 0.000731

Gnomad4 NFE exome AF: 0.00550

Gnomad4 OTH exome AF: 0.00390

GnomAD4 genome AF: 0.00319 AC: 486 AN: 152390 Hom.: 1 Cov.: 34 AF XY: 0.00278 AC XY: 207 AN XY: 74520

Gnomad4 AFR AF: 0.00132

Gnomad4 AMR AF: 0.000914

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.000941

Gnomad4 NFE AF: 0.00495

Gnomad4 OTH AF: 0.00378

Alfa AF: 0.00169 Hom.: 0

Bravo AF: 0.00277

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jun 08, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	4.4
Dann	Benign	0.34

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: rs55669367; hg19: chr11-64597139;