Variant rs3737021 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.2043+18A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 1,534,712 control chromosomes in the GnomAD database, including 15,514 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 0.13 ( 1324 hom., cov: 32)

Exomes 𝑓: 0.14 ( 14190 hom. )

Consequence

DOCK9
NM_001366683.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

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=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.192 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.2043+18A>G		intron_variant		ENST00000682017.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOCK9	ENST00000682017.1 linkuse as main transcript	c.2043+18A>G		intron_variant			NM_001366683.2	P3

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19226

AN:

152048

Hom.:

1321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0769

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.149

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.201

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.151

GnomAD3 exomes

AF:

0.156

AC:

30768

AN:

197014

Hom.:

2674

AF XY:

0.155

AC XY:

16374

AN XY:

105672

show subpopulations

Gnomad AFR exome

AF:

0.0752

Gnomad AMR exome

AF:

0.217

Gnomad ASJ exome

AF:

0.154

Gnomad EAS exome

AF:

0.204

Gnomad SAS exome

AF:

0.198

Gnomad FIN exome

AF:

0.120

Gnomad NFE exome

AF:

0.140

Gnomad OTH exome

AF:

0.149

GnomAD4 exome

AF:

0.139

AC:

191688

AN:

1382544

Hom.:

14190

Cov.:

AF XY:

0.141

AC XY:

96695

AN XY:

687012

show subpopulations

Gnomad4 AFR exome

AF:

0.0724

Gnomad4 AMR exome

AF:

0.206

Gnomad4 ASJ exome

AF:

0.153

Gnomad4 EAS exome

AF:

0.242

Gnomad4 SAS exome

AF:

0.195

Gnomad4 FIN exome

AF:

0.124

Gnomad4 NFE exome

AF:

0.130

Gnomad4 OTH exome

AF:

0.140

GnomAD4 genome

AF:

0.126

AC:

19229

AN:

152168

Hom.:

1324

Cov.:

AF XY:

0.128

AC XY:

9496

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.0769

Gnomad4 AMR

AF:

0.145

Gnomad4 ASJ

AF:

0.149

Gnomad4 EAS

AF:

0.191

Gnomad4 SAS

AF:

0.202

Gnomad4 FIN

AF:

0.114

Gnomad4 NFE

AF:

0.141

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.144

Hom.:

336

Bravo

AF:

0.128

Asia WGS

AF:

0.203

AC:

705

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

Cadd

Benign

1.6

Dann

Benign

0.41

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