chr9-432330-C-G

Variant names:

• chr9-432330-C-G
• rs7036567
• NM_203447.4:c.4785+6C>G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_203447.4(DOCK8):​c.4785+6C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 1,613,316 control chromosomes in the GnomAD database, including 466,623 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.70 (38123 hom., cov: 30)
  • Exomes 𝑓: 0.76 (428500 hom.)
• Consequence: DOCK8 NM_203447.4 splice_region, intron
• Scores: Splicing: ADA: 0.00009776
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:10 O:1
• Conservation: PhyloP100: 0.213

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 9-432330-C-G is Benign according to our data. Variant chr9-432330-C-G is described in ClinVar as [Benign]. Clinvar id is 163176.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-432330-C-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DOCK8	NM_203447.4	c.4785+6C>G		splice_region_variant, intron_variant	Intron 37 of 47	ENST00000432829.7	NP_982272.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DOCK8	ENST00000432829.7	c.4785+6C>G		splice_region_variant, intron_variant	Intron 37 of 47	1	NM_203447.4	ENSP00000394888.3

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105596 AN: 151788 Hom.: 38106 Cov.: 30

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.711

GnomAD3 exomes AF: 0.766 AC: 192546 AN: 251346 Hom.: 75318 AF XY: 0.763 AC XY: 103642 AN XY: 135856

Gnomad AFR exome AF: 0.481

Gnomad AMR exome AF: 0.852

Gnomad ASJ exome AF: 0.712

Gnomad EAS exome AF: 0.985

Gnomad SAS exome AF: 0.688

Gnomad FIN exome AF: 0.795

Gnomad NFE exome AF: 0.766

Gnomad OTH exome AF: 0.757

GnomAD4 exome AF: 0.763 AC: 1114842 AN: 1461410 Hom.: 428500 Cov.: 47 AF XY: 0.761 AC XY: 553218 AN XY: 727042

Gnomad4 AFR exome AF: 0.476

Gnomad4 AMR exome AF: 0.845

Gnomad4 ASJ exome AF: 0.713

Gnomad4 EAS exome AF: 0.980

Gnomad4 SAS exome AF: 0.689

Gnomad4 FIN exome AF: 0.794

Gnomad4 NFE exome AF: 0.766

Gnomad4 OTH exome AF: 0.757

GnomAD4 genome AF: 0.696 AC: 105662 AN: 151906 Hom.: 38123 Cov.: 30 AF XY: 0.700 AC XY: 51954 AN XY: 74238

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.713

Alfa AF: 0.730 Hom.: 10715

Bravo AF: 0.690

Asia WGS AF: 0.823 AC: 2862 AN: 3478

EpiCase AF: 0.751

EpiControl AF: 0.763

ClinVar

Significance: Benign

Submissions summary: Benign:10 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:5

Nov 12, 2023

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 96% of patients studied by a panel of primary immunodeficiencies. Number of patients: 92. Only high quality variants are reported. -

-

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Feb 21, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

4785+6C>G in intron 37 of DOCK8: This variant is not expected to have clinical s ignificance because it has been identified in 49.3% (2171/4406) of African Ameri can chromosomes from a broad population by the NHLBI Exome Sequencing Project (h ttp://evs.gs.washington.edu/EVS; dbSNP rs7036567). -

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PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided Benign:2 Other:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

-

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Combined immunodeficiency due to DOCK8 deficiency Benign:2

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.6
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000098
dbscSNV1_RF	Benign	0.042
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: rs7036567; hg19: chr9-432330;