Variant rs2296990 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.4013+41C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0588 in 1,415,940 control chromosomes in the GnomAD database, including 3,695 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 0.051 ( 341 hom., cov: 32)

Exomes 𝑓: 0.060 ( 3354 hom. )

Consequence

DOCK9
NM_001366683.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.601

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:

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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 = 0.174 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.4013+41C>T		intron_variant		ENST00000682017.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOCK9	ENST00000682017.1 linkuse as main transcript	c.4013+41C>T		intron_variant			NM_001366683.2	P3

Frequencies

GnomAD3 genomes

AF:

0.0515

AC:

7822

AN:

151994

Hom.:

339

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0156

Gnomad AMI

AF:

0.0954

Gnomad AMR

AF:

0.0915

Gnomad ASJ

AF:

0.0591

Gnomad EAS

AF:

0.184

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.0413

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0496

Gnomad OTH

AF:

0.0688

GnomAD3 exomes

AF:

0.0820

AC:

13162

AN:

160464

Hom.:

785

AF XY:

0.0798

AC XY:

6767

AN XY:

84816

show subpopulations

Gnomad AFR exome

AF:

0.0152

Gnomad AMR exome

AF:

0.167

Gnomad ASJ exome

AF:

0.0639

Gnomad EAS exome

AF:

0.179

Gnomad SAS exome

AF:

0.0998

Gnomad FIN exome

AF:

0.0414

Gnomad NFE exome

AF:

0.0504

Gnomad OTH exome

AF:

0.0721

GnomAD4 exome

AF:

0.0597

AC:

75417

AN:

1263826

Hom.:

3354

Cov.:

AF XY:

0.0607

AC XY:

38257

AN XY:

630180

show subpopulations

Gnomad4 AFR exome

AF:

0.0141

Gnomad4 AMR exome

AF:

0.154

Gnomad4 ASJ exome

AF:

0.0665

Gnomad4 EAS exome

AF:

0.238

Gnomad4 SAS exome

AF:

0.103

Gnomad4 FIN exome

AF:

0.0406

Gnomad4 NFE exome

AF:

0.0481

Gnomad4 OTH exome

AF:

0.0616

GnomAD4 genome

AF:

0.0514

AC:

7826

AN:

152114

Hom.:

341

Cov.:

AF XY:

0.0540

AC XY:

4018

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.0156

Gnomad4 AMR

AF:

0.0917

Gnomad4 ASJ

AF:

0.0591

Gnomad4 EAS

AF:

0.184

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.0413

Gnomad4 NFE

AF:

0.0496

Gnomad4 OTH

AF:

0.0691

Alfa

AF:

0.0571

Hom.:

104

Bravo

AF:

0.0581

Asia WGS

AF:

0.148

AC:

514

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

7.6

DANN

Benign

0.70

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