rs3818287

Positions:

• chr14-102964210-C-A
• chr14-102964210-C-G
• chr14-102964210-C-T

Variant summary

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

The NM_006035.4(CDC42BPB):​c.2726+292G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,256 control chromosomes in the GnomAD database, including 1,918 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 0.15 (1918 hom., cov: 33)
• Consequence: CDC42BPB NM_006035.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

Genes affected

CDC42BPB (HGNC:1738): (CDC42 binding protein kinase beta) This gene encodes a member of the serine/threonine protein kinase family. The encoded protein contains a Cdc42/Rac-binding p21 binding domain resembling that of PAK kinase. The kinase domain of this protein is most closely related to that of myotonic dystrophy kinase-related ROK. Studies of the similar gene in rat suggested that this kinase may act as a downstream effector of Cdc42 in cytoskeletal reorganization. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDC42BPB	NM_006035.4	c.2726+292G>T		intron_variant		ENST00000361246.7	NP_006026.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDC42BPB	ENST00000361246.7	c.2726+292G>T		intron_variant		1	NM_006035.4	ENSP00000355237.2
CDC42BPB	ENST00000559043.2	c.2726+292G>T		intron_variant		5		ENSP00000453384.2

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23401 AN: 152138 Hom.: 1915 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.154 AC: 23416 AN: 152256 Hom.: 1918 Cov.: 33 AF XY: 0.154 AC XY: 11444 AN XY: 74454

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0870

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.153

Alfa AF: 0.129 Hom.: 950

Bravo AF: 0.154

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.74
DANN	Benign	0.66

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: rs3818287; hg19: chr14-103430547;