Variant rs11207993 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001367561.1(DOCK7):c.2010+35G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 1,475,086 control chromosomes in the GnomAD database, including 20,697 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1433 hom., cov: 28)

Exomes 𝑓: 0.17 ( 19264 hom. )

Consequence

DOCK7
NM_001367561.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.56

Variant links:

Genes affected

DOCK7 (HGNC:19190): (dedicator of cytokinesis 7) The protein encoded by this gene is a guanine nucleotide exchange factor (GEF) that plays a role in axon formation and neuronal polarization. The encoded protein displays GEF activity toward RAC1 and RAC3 Rho small GTPases but not toward CDC42. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

DOCK7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 1-62578793-C-T is Benign according to our data. Variant chr1-62578793-C-T is described in ClinVar as [Benign]. Clinvar id is 1296220.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DOCK7	NM_001367561.1 linkuse as main transcript	c.2010+35G>A		intron_variant		ENST00000635253.2	NP_001354490.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DOCK7	ENST00000635253.2 linkuse as main transcript	c.2010+35G>A		intron_variant		5	NM_001367561.1	ENSP00000489124		Q96N67-1

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

18968

AN:

148726

Hom.:

1432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0556

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.000787

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.173

Gnomad OTH

AF:

0.113

GnomAD3 exomes

AF:

0.140

AC:

27538

AN:

196066

Hom.:

2298

AF XY:

0.141

AC XY:

15161

AN XY:

107566

show subpopulations

Gnomad AFR exome

AF:

0.0515

Gnomad AMR exome

AF:

0.183

Gnomad ASJ exome

AF:

0.117

Gnomad EAS exome

AF:

0.00121

Gnomad SAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.150

Gnomad NFE exome

AF:

0.169

Gnomad OTH exome

AF:

0.136

GnomAD4 exome

AF:

0.166

AC:

219962

AN:

1326312

Hom.:

19264

Cov.:

AF XY:

0.164

AC XY:

108364

AN XY:

660346

show subpopulations

Gnomad4 AFR exome

AF:

0.0483

Gnomad4 AMR exome

AF:

0.182

Gnomad4 ASJ exome

AF:

0.120

Gnomad4 EAS exome

AF:

0.000614

Gnomad4 SAS exome

AF:

0.118

Gnomad4 FIN exome

AF:

0.158

Gnomad4 NFE exome

AF:

0.180

Gnomad4 OTH exome

AF:

0.145

GnomAD4 genome

AF:

0.128

AC:

18969

AN:

148774

Hom.:

1433

Cov.:

AF XY:

0.127

AC XY:

9184

AN XY:

72276

show subpopulations

Gnomad4 AFR

AF:

0.0554

Gnomad4 AMR

AF:

0.156

Gnomad4 ASJ

AF:

0.116

Gnomad4 EAS

AF:

0.000986

Gnomad4 SAS

AF:

0.108

Gnomad4 FIN

AF:

0.148

Gnomad4 NFE

AF:

0.173

Gnomad4 OTH

AF:

0.111

Alfa

AF:

0.159

Hom.:

2801

Bravo

AF:

0.126

Asia WGS

AF:

0.0550

AC:

193

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 14, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jul 15, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 28% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 26. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.093

DANN

Benign

0.30

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