Variant rs9557078 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.5514+24T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 1,568,862 control chromosomes in the GnomAD database, including 140,170 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 0.41 ( 13458 hom., cov: 32)

Exomes 𝑓: 0.42 ( 126712 hom. )

Consequence

DOCK9
NM_001366683.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0520

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=-0.72).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 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.5514+24T>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.5514+24T>G		intron_variant			NM_001366683.2	P3

Frequencies

GnomAD3 genomes

AF:

0.413

AC:

62758

AN:

151920

Hom.:

13446

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.333

Gnomad AMR

AF:

0.327

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.674

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.494

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.431

Gnomad OTH

AF:

0.400

GnomAD3 exomes

AF:

0.420

AC:

102624

AN:

244190

Hom.:

22659

AF XY:

0.416

AC XY:

55182

AN XY:

132494

show subpopulations

Gnomad AFR exome

AF:

0.373

Gnomad AMR exome

AF:

0.330

Gnomad ASJ exome

AF:

0.390

Gnomad EAS exome

AF:

0.679

Gnomad SAS exome

AF:

0.315

Gnomad FIN exome

AF:

0.491

Gnomad NFE exome

AF:

0.430

Gnomad OTH exome

AF:

0.400

GnomAD4 exome

AF:

0.417

AC:

591175

AN:

1416824

Hom.:

126712

Cov.:

AF XY:

0.415

AC XY:

290534

AN XY:

699722

show subpopulations

Gnomad4 AFR exome

AF:

0.371

Gnomad4 AMR exome

AF:

0.325

Gnomad4 ASJ exome

AF:

0.385

Gnomad4 EAS exome

AF:

0.678

Gnomad4 SAS exome

AF:

0.316

Gnomad4 FIN exome

AF:

0.488

Gnomad4 NFE exome

AF:

0.418

Gnomad4 OTH exome

AF:

0.411

GnomAD4 genome

AF:

0.413

AC:

62813

AN:

152038

Hom.:

13458

Cov.:

AF XY:

0.414

AC XY:

30793

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.376

Gnomad4 AMR

AF:

0.326

Gnomad4 ASJ

AF:

0.386

Gnomad4 EAS

AF:

0.674

Gnomad4 SAS

AF:

0.337

Gnomad4 FIN

AF:

0.494

Gnomad4 NFE

AF:

0.431

Gnomad4 OTH

AF:

0.400

Alfa

AF:

0.422

Hom.:

21691

Bravo

AF:

0.398

Asia WGS

AF:

0.452

AC:

1574

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

4.3

DANN

Benign

0.80

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