Variant rs541344421 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_001367561.1(DOCK7):c.1283-14delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00809 in 1,515,688 control chromosomes in the GnomAD database, including 52 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0053 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0084 ( 50 hom. )

Consequence

DOCK7
NM_001367561.1 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -3.26

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 -16 ACMG points.

BP6

Variant 1-62625414-TA-T is Benign according to our data. Variant chr1-62625414-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 235780.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00533 (804/150782) while in subpopulation NFE AF= 0.00827 (559/67568). AF 95% confidence interval is 0.00771. There are 2 homozygotes in gnomad4. There are 368 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DOCK7	NM_001367561.1 linkuse as main transcript	c.1283-14delT		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.1283-14delT		intron_variant		5	NM_001367561.1	ENSP00000489124.1		Q96N67-1

Frequencies

GnomAD3 genomes

AF:

0.00534

AC:

804

AN:

150676

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00163

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00410

Gnomad ASJ

AF:

0.00581

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000838

Gnomad FIN

AF:

0.00798

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00827

Gnomad OTH

AF:

0.00435

GnomAD3 exomes

AF:

0.00659

AC:

1234

AN:

187348

Hom.:

AF XY:

0.00682

AC XY:

697

AN XY:

102176

show subpopulations

Gnomad AFR exome

AF:

0.00148

Gnomad AMR exome

AF:

0.00287

Gnomad ASJ exome

AF:

0.00832

Gnomad EAS exome

AF:

0.000975

Gnomad SAS exome

AF:

0.00110

Gnomad FIN exome

AF:

0.00816

Gnomad NFE exome

AF:

0.00956

Gnomad OTH exome

AF:

0.00983

GnomAD4 exome

AF:

0.00839

AC:

11457

AN:

1364906

Hom.:

Cov.:

AF XY:

0.00822

AC XY:

5559

AN XY:

676582

show subpopulations

Gnomad4 AFR exome

AF:

0.00174

Gnomad4 AMR exome

AF:

0.00243

Gnomad4 ASJ exome

AF:

0.00644

Gnomad4 EAS exome

AF:

0.000320

Gnomad4 SAS exome

AF:

0.00132

Gnomad4 FIN exome

AF:

0.00789

Gnomad4 NFE exome

AF:

0.00974

Gnomad4 OTH exome

AF:

0.00705

GnomAD4 genome

AF:

0.00533

AC:

804

AN:

150782

Hom.:

Cov.:

AF XY:

0.00500

AC XY:

368

AN XY:

73618

show subpopulations

Gnomad4 AFR

AF:

0.00163

Gnomad4 AMR

AF:

0.00410

Gnomad4 ASJ

AF:

0.00581

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000839

Gnomad4 FIN

AF:

0.00798

Gnomad4 NFE

AF:

0.00827

Gnomad4 OTH

AF:

0.00431

Alfa

AF:

0.00504

Hom.:

Bravo

AF:

0.00499

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy, 23

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 28, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Apr 11, 2023	- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Feb 02, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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