Variant chr13-98810339-C-T 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.5131-48G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 1,600,096 control chromosomes in the GnomAD database, including 135,864 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 0.35 ( 10842 hom., cov: 31)

Exomes 𝑓: 0.41 ( 125022 hom. )

Consequence

DOCK9
NM_001366683.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.79

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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.5131-48G>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.5131-48G>A		intron_variant			NM_001366683.2	P3

Frequencies

GnomAD3 genomes

AF:

0.350

AC:

53120

AN:

151864

Hom.:

10840

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.334

Gnomad AMR

AF:

0.301

Gnomad ASJ

AF:

0.384

Gnomad EAS

AF:

0.673

Gnomad SAS

AF:

0.319

Gnomad FIN

AF:

0.494

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.427

Gnomad OTH

AF:

0.348

GnomAD3 exomes

AF:

0.399

AC:

95571

AN:

239688

Hom.:

20722

AF XY:

0.398

AC XY:

51904

AN XY:

130574

show subpopulations

Gnomad AFR exome

AF:

0.154

Gnomad AMR exome

AF:

0.317

Gnomad ASJ exome

AF:

0.388

Gnomad EAS exome

AF:

0.677

Gnomad SAS exome

AF:

0.297

Gnomad FIN exome

AF:

0.494

Gnomad NFE exome

AF:

0.427

Gnomad OTH exome

AF:

0.388

GnomAD4 exome

AF:

0.408

AC:

590675

AN:

1448114

Hom.:

125022

Cov.:

AF XY:

0.406

AC XY:

292418

AN XY:

719598

show subpopulations

Gnomad4 AFR exome

AF:

0.153

Gnomad4 AMR exome

AF:

0.311

Gnomad4 ASJ exome

AF:

0.385

Gnomad4 EAS exome

AF:

0.678

Gnomad4 SAS exome

AF:

0.302

Gnomad4 FIN exome

AF:

0.488

Gnomad4 NFE exome

AF:

0.416

Gnomad4 OTH exome

AF:

0.393

GnomAD4 genome

AF:

0.350

AC:

53148

AN:

151982

Hom.:

10842

Cov.:

AF XY:

0.352

AC XY:

26170

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.165

Gnomad4 AMR

AF:

0.301

Gnomad4 ASJ

AF:

0.384

Gnomad4 EAS

AF:

0.673

Gnomad4 SAS

AF:

0.320

Gnomad4 FIN

AF:

0.494

Gnomad4 NFE

AF:

0.427

Gnomad4 OTH

AF:

0.348

Alfa

AF:

0.385

Hom.:

2638

Bravo

AF:

0.328

Asia WGS

AF:

0.430

AC:

1497

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.054

DANN

Benign

0.50

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