Variant rs12429249 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001366683.2(DOCK9):c.334-46G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,454,830 control chromosomes in the GnomAD database, including 22,546 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 ( 1971 hom., cov: 33)

Exomes 𝑓: 0.18 ( 20575 hom. )

Consequence

DOCK9
NM_001366683.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.33

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 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.334-46G>A		intron_variant		ENST00000682017.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOCK9	ENST00000682017.1 linkuse as main transcript	c.334-46G>A		intron_variant			NM_001366683.2	P3

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

23261

AN:

152048

Hom.:

1970

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0863

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.172

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.177

GnomAD3 exomes

AF:

0.188

AC:

23839

AN:

126960

Hom.:

2323

AF XY:

0.186

AC XY:

12606

AN XY:

67662

show subpopulations

Gnomad AFR exome

AF:

0.0844

Gnomad AMR exome

AF:

0.231

Gnomad ASJ exome

AF:

0.178

Gnomad EAS exome

AF:

0.204

Gnomad SAS exome

AF:

0.209

Gnomad FIN exome

AF:

0.176

Gnomad NFE exome

AF:

0.183

Gnomad OTH exome

AF:

0.173

GnomAD4 exome

AF:

0.176

AC:

228739

AN:

1302662

Hom.:

20575

Cov.:

AF XY:

0.176

AC XY:

113674

AN XY:

644156

show subpopulations

Gnomad4 AFR exome

AF:

0.0810

Gnomad4 AMR exome

AF:

0.215

Gnomad4 ASJ exome

AF:

0.175

Gnomad4 EAS exome

AF:

0.245

Gnomad4 SAS exome

AF:

0.208

Gnomad4 FIN exome

AF:

0.170

Gnomad4 NFE exome

AF:

0.173

Gnomad4 OTH exome

AF:

0.173

GnomAD4 genome

AF:

0.153

AC:

23270

AN:

152168

Hom.:

1971

Cov.:

AF XY:

0.153

AC XY:

11415

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.0864

Gnomad4 AMR

AF:

0.164

Gnomad4 ASJ

AF:

0.172

Gnomad4 EAS

AF:

0.193

Gnomad4 SAS

AF:

0.213

Gnomad4 FIN

AF:

0.158

Gnomad4 NFE

AF:

0.181

Gnomad4 OTH

AF:

0.177

Alfa

AF:

0.178

Hom.:

5080

Bravo

AF:

0.152

Asia WGS

AF:

0.208

AC:

723

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.15

DANN

Benign

0.32

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