Variant 13-98797235-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001366683.2(DOCK9):c.6036C>T(p.Cys2012=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00547 in 1,613,846 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0050 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0055 ( 33 hom. )

Consequence

DOCK9
NM_001366683.2 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.131

Variant links:

Genes affected

DOCK9 (HGNC:14132): (dedicator of cytokinesis 9) Enables cadherin binding activity. Predicted to be involved in positive regulation of GTPase activity. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

DOCK9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 13-98797235-G-A is Benign according to our data. Variant chr13-98797235-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 790370.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.131 with no splicing effect.

BS2

High Homozygotes in GnomAdExome at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DOCK9	NM_001366683.2 linkuse as main transcript	c.6036C>T	p.Cys2012=	synonymous_variant	52/53	ENST00000682017.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOCK9	ENST00000682017.1 linkuse as main transcript	c.6036C>T	p.Cys2012=	synonymous_variant	52/53		NM_001366683.2	P3

Frequencies

GnomAD3 genomes

AF:

0.00503

AC:

765

AN:

152108

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00162

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.00629

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00373

Gnomad FIN

AF:

0.00764

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00666

Gnomad OTH

AF:

0.0101

GnomAD3 exomes

AF:

0.00459

AC:

1144

AN:

249008

Hom.:

AF XY:

0.00470

AC XY:

635

AN XY:

135124

show subpopulations

Gnomad AFR exome

AF:

0.00207

Gnomad AMR exome

AF:

0.00479

Gnomad ASJ exome

AF:

0.00199

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00298

Gnomad FIN exome

AF:

0.00719

Gnomad NFE exome

AF:

0.00579

Gnomad OTH exome

AF:

0.00447

GnomAD4 exome

AF:

0.00552

AC:

8070

AN:

1461620

Hom.:

Cov.:

AF XY:

0.00540

AC XY:

3925

AN XY:

727076

show subpopulations

Gnomad4 AFR exome

AF:

0.00170

Gnomad4 AMR exome

AF:

0.00505

Gnomad4 ASJ exome

AF:

0.00222

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00300

Gnomad4 FIN exome

AF:

0.00551

Gnomad4 NFE exome

AF:

0.00610

Gnomad4 OTH exome

AF:

0.00571

GnomAD4 genome

AF:

0.00503

AC:

765

AN:

152226

Hom.:

Cov.:

AF XY:

0.00536

AC XY:

399

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.00161

Gnomad4 AMR

AF:

0.00628

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00374

Gnomad4 FIN

AF:

0.00764

Gnomad4 NFE

AF:

0.00666

Gnomad4 OTH

AF:

0.00995

Alfa

AF:

0.00604

Hom.:

Bravo

AF:

0.00496

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00632

EpiControl

AF:

0.00623

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2023	DOCK9: BP4, BP7, BS2 -
Benign, criteria provided, single submitter	clinical testing	Invitae	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

Cadd

Benign

0.084

Dann

Benign

0.57

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