Variant rs2274643 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.1978-23T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 1,605,090 control chromosomes in the GnomAD database, including 269,571 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 0.53 ( 21769 hom., cov: 32)

Exomes 𝑓: 0.58 ( 247802 hom. )

Consequence

DOCK9
NM_001366683.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.241

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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 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.1978-23T>C		intron_variant		ENST00000682017.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOCK9	ENST00000682017.1 linkuse as main transcript	c.1978-23T>C		intron_variant			NM_001366683.2	P3

Frequencies

GnomAD3 genomes

AF:

0.528

AC:

80285

AN:

151924

Hom.:

21768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.433

Gnomad AMI

AF:

0.641

Gnomad AMR

AF:

0.563

Gnomad ASJ

AF:

0.575

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.541

Gnomad FIN

AF:

0.556

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.584

Gnomad OTH

AF:

0.561

GnomAD3 exomes

AF:

0.543

AC:

129674

AN:

238768

Hom.:

35882

AF XY:

0.550

AC XY:

71164

AN XY:

129384

show subpopulations

Gnomad AFR exome

AF:

0.431

Gnomad AMR exome

AF:

0.524

Gnomad ASJ exome

AF:

0.580

Gnomad EAS exome

AF:

0.320

Gnomad SAS exome

AF:

0.562

Gnomad FIN exome

AF:

0.558

Gnomad NFE exome

AF:

0.586

Gnomad OTH exome

AF:

0.575

GnomAD4 exome

AF:

0.581

AC:

843578

AN:

1453048

Hom.:

247802

Cov.:

AF XY:

0.580

AC XY:

418720

AN XY:

722382

show subpopulations

Gnomad4 AFR exome

AF:

0.424

Gnomad4 AMR exome

AF:

0.531

Gnomad4 ASJ exome

AF:

0.582

Gnomad4 EAS exome

AF:

0.341

Gnomad4 SAS exome

AF:

0.560

Gnomad4 FIN exome

AF:

0.558

Gnomad4 NFE exome

AF:

0.599

Gnomad4 OTH exome

AF:

0.569

GnomAD4 genome

AF:

0.528

AC:

80309

AN:

152042

Hom.:

21769

Cov.:

AF XY:

0.525

AC XY:

39043

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.432

Gnomad4 AMR

AF:

0.562

Gnomad4 ASJ

AF:

0.575

Gnomad4 EAS

AF:

0.329

Gnomad4 SAS

AF:

0.540

Gnomad4 FIN

AF:

0.556

Gnomad4 NFE

AF:

0.584

Gnomad4 OTH

AF:

0.564

Alfa

AF:

0.549

Hom.:

4763

Bravo

AF:

0.528

Asia WGS

AF:

0.449

AC:

1560

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

Cadd

Benign

2.2

Dann

Benign

0.48

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