Variant 13-98805177-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001366683.2(DOCK9):c.5547A>C(p.Ala1849=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 1,602,684 control chromosomes in the GnomAD database, including 32,263 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 0.20 ( 3169 hom., cov: 32)

Exomes 𝑓: 0.20 ( 29094 hom. )

Consequence

DOCK9
NM_001366683.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -8.87

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.05).

BP7

Synonymous conserved (PhyloP=-8.87 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DOCK9	NM_001366683.2 linkuse as main transcript	c.5547A>C	p.Ala1849=	synonymous_variant	49/53	ENST00000682017.1	NP_001353612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DOCK9	ENST00000682017.1 linkuse as main transcript	c.5547A>C	p.Ala1849=	synonymous_variant	49/53		NM_001366683.2	ENSP00000507034	P3

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30933

AN:

152090

Hom.:

3164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.201

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.191

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.205

Gnomad OTH

AF:

0.214

GnomAD3 exomes

AF:

0.206

AC:

47876

AN:

232188

Hom.:

4935

AF XY:

0.204

AC XY:

25546

AN XY:

125352

show subpopulations

Gnomad AFR exome

AF:

0.217

Gnomad AMR exome

AF:

0.226

Gnomad ASJ exome

AF:

0.190

Gnomad EAS exome

AF:

0.191

Gnomad SAS exome

AF:

0.209

Gnomad FIN exome

AF:

0.198

Gnomad NFE exome

AF:

0.204

Gnomad OTH exome

AF:

0.196

GnomAD4 exome

AF:

0.200

AC:

289877

AN:

1450474

Hom.:

29094

Cov.:

AF XY:

0.200

AC XY:

144304

AN XY:

720308

show subpopulations

Gnomad4 AFR exome

AF:

0.215

Gnomad4 AMR exome

AF:

0.218

Gnomad4 ASJ exome

AF:

0.187

Gnomad4 EAS exome

AF:

0.238

Gnomad4 SAS exome

AF:

0.210

Gnomad4 FIN exome

AF:

0.201

Gnomad4 NFE exome

AF:

0.197

Gnomad4 OTH exome

AF:

0.197

GnomAD4 genome

AF:

0.203

AC:

30952

AN:

152210

Hom.:

3169

Cov.:

AF XY:

0.203

AC XY:

15099

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.214

Gnomad4 AMR

AF:

0.173

Gnomad4 ASJ

AF:

0.177

Gnomad4 EAS

AF:

0.191

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.198

Gnomad4 NFE

AF:

0.205

Gnomad4 OTH

AF:

0.213

Alfa

AF:

0.204

Hom.:

7002

Bravo

AF:

0.202

Asia WGS

AF:

0.214

AC:

741

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.28

DANN

Benign

0.40

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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