Variant rs12348944 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_203447.4(DOCK8):c.2295C>T(p.Ser765=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 1,613,360 control chromosomes in the GnomAD database, including 361 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.031 ( 135 hom., cov: 33)

Exomes 𝑓: 0.012 ( 226 hom. )

Consequence

DOCK8
NM_203447.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -2.81

Variant links:

Genes affected

DOCK8 (HGNC:19191): (dedicator of cytokinesis 8) This gene encodes a member of the DOCK180 family of guanine nucleotide exchange factors. Guanine nucleotide exchange factors interact with Rho GTPases and are components of intracellular signaling networks. Mutations in this gene result in the autosomal recessive form of the hyper-IgE syndrome. Alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Jun 2010]

DOCK8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 9-377066-C-T is Benign according to our data. Variant chr9-377066-C-T is described in ClinVar as [Benign]. Clinvar id is 137138.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-377066-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-2.81 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DOCK8	NM_203447.4 linkuse as main transcript	c.2295C>T	p.Ser765=	synonymous_variant	20/48	ENST00000432829.7	NP_982272.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DOCK8	ENST00000432829.7 linkuse as main transcript	c.2295C>T	p.Ser765=	synonymous_variant	20/48	1	NM_203447.4	ENSP00000394888		Q8NF50-1

Frequencies

GnomAD3 genomes

AF:

0.0306

AC:

4653

AN:

152182

Hom.:

136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0807

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0195

Gnomad ASJ

AF:

0.00692

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.00849

Gnomad FIN

AF:

0.00443

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0123

Gnomad OTH

AF:

0.0254

GnomAD3 exomes

AF:

0.0146

AC:

3645

AN:

250216

Hom.:

AF XY:

0.0134

AC XY:

1808

AN XY:

135334

show subpopulations

Gnomad AFR exome

AF:

0.0824

Gnomad AMR exome

AF:

0.0134

Gnomad ASJ exome

AF:

0.00506

Gnomad EAS exome

AF:

0.000382

Gnomad SAS exome

AF:

0.00945

Gnomad FIN exome

AF:

0.00420

Gnomad NFE exome

AF:

0.0116

Gnomad OTH exome

AF:

0.0163

GnomAD4 exome

AF:

0.0123

AC:

18013

AN:

1461060

Hom.:

226

Cov.:

AF XY:

0.0119

AC XY:

8668

AN XY:

726854

show subpopulations

Gnomad4 AFR exome

AF:

0.0826

Gnomad4 AMR exome

AF:

0.0140

Gnomad4 ASJ exome

AF:

0.00494

Gnomad4 EAS exome

AF:

0.000176

Gnomad4 SAS exome

AF:

0.00946

Gnomad4 FIN exome

AF:

0.00427

Gnomad4 NFE exome

AF:

0.0112

Gnomad4 OTH exome

AF:

0.0144

GnomAD4 genome

AF:

0.0306

AC:

4655

AN:

152300

Hom.:

135

Cov.:

AF XY:

0.0290

AC XY:

2163

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0805

Gnomad4 AMR

AF:

0.0195

Gnomad4 ASJ

AF:

0.00692

Gnomad4 EAS

AF:

0.000385

Gnomad4 SAS

AF:

0.00849

Gnomad4 FIN

AF:

0.00443

Gnomad4 NFE

AF:

0.0123

Gnomad4 OTH

AF:

0.0251

Alfa

AF:

0.0166

Hom.:

Bravo

AF:

0.0330

Asia WGS

AF:

0.00953

AC:

AN:

3478

EpiCase

AF:

0.0133

EpiControl

AF:

0.0111

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 20, 2014	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 21, 2013	Ser765Ser in exon 20 of DOCK8: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 7.6% (335/4406) of African American chromosomes from a broad population by the NHLBI Exome Sequenci ng Project (http://evs.gs.washington.edu/EVS; dbSNP rs12348944). -

Autosomal recessive hyper-IgE syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Combined immunodeficiency due to DOCK8 deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

0.18

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over