rs9513497

chr13-98853378-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366683.2(DOCK9):c.3946+30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 1,464,336 control chromosomes in the GnomAD database, including 190,053 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 0.47 (17452 hom., cov: 32)
  • Exomes 𝑓: 0.51 (172601 hom.)
• Consequence: DOCK9 NM_001366683.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DOCK9	NM_001366683.2	c.3946+30G>A		intron_variant		ENST00000682017.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOCK9	ENST00000682017.1	c.3946+30G>A		intron_variant			NM_001366683.2	P3

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72014 AN: 151830 Hom.: 17454 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.496

GnomAD3 exomes AF: 0.475 AC: 106631 AN: 224638 Hom.: 26145 AF XY: 0.476 AC XY: 58106 AN XY: 121970

Gnomad AFR exome AF: 0.401

Gnomad AMR exome AF: 0.496

Gnomad ASJ exome AF: 0.471

Gnomad EAS exome AF: 0.269

Gnomad SAS exome AF: 0.430

Gnomad FIN exome AF: 0.506

Gnomad NFE exome AF: 0.514

Gnomad OTH exome AF: 0.506

GnomAD4 exome AF: 0.508 AC: 666325 AN: 1312388 Hom.: 172601 Cov.: 17 AF XY: 0.505 AC XY: 332352 AN XY: 658124

Gnomad4 AFR exome AF: 0.398

Gnomad4 AMR exome AF: 0.501

Gnomad4 ASJ exome AF: 0.469

Gnomad4 EAS exome AF: 0.251

Gnomad4 SAS exome AF: 0.434

Gnomad4 FIN exome AF: 0.509

Gnomad4 NFE exome AF: 0.528

Gnomad4 OTH exome AF: 0.496

GnomAD4 genome AF: 0.474 AC: 72031 AN: 151948 Hom.: 17452 Cov.: 32 AF XY: 0.472 AC XY: 35066 AN XY: 74262

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.497

Alfa AF: 0.491 Hom.: 6407

Bravo AF: 0.477

Asia WGS AF: 0.357 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.8
Dann	Benign	0.60

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

Other links and lift over

dbSNP: rs9513497; hg19: chr13-99505632;