chr9-463276-TA-T

Position:

• chr9-463276-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_203447.4(DOCK8):​c.6069-229delA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (17786 hom., cov: 0)
• Consequence: DOCK8 NM_203447.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.327

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-AS2 (HGNC:55822): (DOCK8 antisense RNA 2)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 9-463276-TA-T is Benign according to our data. Variant chr9-463276-TA-T is described in ClinVar as [Benign]. Clinvar id is 1230014.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DOCK8	NM_203447.4	c.6069-229delA		intron_variant		ENST00000432829.7	NP_982272.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DOCK8	ENST00000432829.7	c.6069-240delA		intron_variant		1	NM_203447.4	ENSP00000394888.3

Frequencies

GnomAD3 genomes AF: 0.477 AC: 70733 AN: 148416 Hom.: 17781 Cov.: 0

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.476 AC: 70761 AN: 148514 Hom.: 17786 Cov.: 0 AF XY: 0.476 AC XY: 34472 AN XY: 72360

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.473

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

GeneDx

Sep 12, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs5895846; hg19: chr9-463276;