Variant rs12428661 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001366683.2(DOCK9):c.474C>T(p.Val158=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 1,612,214 control chromosomes in the GnomAD database, including 23,051 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.15 ( 1851 hom., cov: 33)

Exomes 𝑓: 0.17 ( 21200 hom. )

Consequence

DOCK9
NM_001366683.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.571

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP7

Synonymous conserved (PhyloP=-0.571 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DOCK9	NM_001366683.2 linkuse as main transcript	c.474C>T	p.Val158=	synonymous_variant	5/53	ENST00000682017.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOCK9	ENST00000682017.1 linkuse as main transcript	c.474C>T	p.Val158=	synonymous_variant	5/53		NM_001366683.2	P3

Frequencies

GnomAD3 genomes

AF:

0.149

AC:

22616

AN:

152032

Hom.:

1850

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0890

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.173

GnomAD3 exomes

AF:

0.181

AC:

45108

AN:

248996

Hom.:

4373

AF XY:

0.181

AC XY:

24395

AN XY:

135080

show subpopulations

Gnomad AFR exome

AF:

0.0883

Gnomad AMR exome

AF:

0.236

Gnomad ASJ exome

AF:

0.174

Gnomad EAS exome

AF:

0.199

Gnomad SAS exome

AF:

0.205

Gnomad FIN exome

AF:

0.164

Gnomad NFE exome

AF:

0.172

Gnomad OTH exome

AF:

0.170

GnomAD4 exome

AF:

0.167

AC:

244533

AN:

1460064

Hom.:

21200

Cov.:

AF XY:

0.169

AC XY:

122546

AN XY:

726410

show subpopulations

Gnomad4 AFR exome

AF:

0.0849

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.173

Gnomad4 EAS exome

AF:

0.242

Gnomad4 SAS exome

AF:

0.204

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.162

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.149

AC:

22633

AN:

152150

Hom.:

1851

Cov.:

AF XY:

0.149

AC XY:

11115

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.0893

Gnomad4 AMR

AF:

0.161

Gnomad4 ASJ

AF:

0.171

Gnomad4 EAS

AF:

0.194

Gnomad4 SAS

AF:

0.212

Gnomad4 FIN

AF:

0.157

Gnomad4 NFE

AF:

0.171

Gnomad4 OTH

AF:

0.172

Alfa

AF:

0.146

Hom.:

941

Bravo

AF:

0.148

EpiCase

AF:

0.173

EpiControl

AF:

0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

2.9

DANN

Benign

0.68

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over