14-102964210-C-A

Variant names:

• chr14-102964210-C-A
• rs3818287
• NM_006035.4:c.2726+292G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

CDC42BPB Gene-Disease associations (from GenCC):

• Chilton-Okur-Chung neurodevelopmental syndrome

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P
• complex neurodevelopmental disorder

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CDC42BPB	NM_006035.4	c.2726+292G>T		intron_variant	Intron 19 of 36	ENST00000361246.7	NP_006026.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC42BPB	ENST00000361246.7	c.2726+292G>T		intron_variant	Intron 19 of 36	1	NM_006035.4	ENSP00000355237.2
CDC42BPB	ENST00000559043.2	c.2726+292G>T		intron_variant	Intron 19 of 35	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

African (AFR) AF: 0.165 AC: 6839 AN: 41542

American (AMR) AF: 0.132 AC: 2025 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 302 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1442 AN: 5174

South Asian (SAS) AF: 0.103 AC: 497 AN: 4828

European-Finnish (FIN) AF: 0.204 AC: 2161 AN: 10606

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9668 AN: 68016

Other (OTH) AF: 0.153 AC: 324 AN: 2116

Alfa AF: 0.132 Hom.: 1138

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
PhyloP100		-0.79
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: rs3818287; hg19: chr14-103430547;