13-98888141-A-G

Position:

• chr13-98888141-A-G

Variant summary

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

The NM_001366683.2(DOCK9):​c.2043+17T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 1,556,262 control chromosomes in the GnomAD database, including 457,611 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 0.71 (38897 hom., cov: 32)
  • Exomes 𝑓: 0.77 (418714 hom.)
• Consequence: DOCK9 NM_001366683.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DOCK9	NM_001366683.2	c.2043+17T>C		intron_variant		ENST00000682017.1	NP_001353612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DOCK9	ENST00000682017.1	c.2043+17T>C		intron_variant			NM_001366683.2	ENSP00000507034.1

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107476 AN: 151952 Hom.: 38877 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.895

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.757

GnomAD3 exomes AF: 0.752 AC: 147971 AN: 196662 Hom.: 56508 AF XY: 0.761 AC XY: 80247 AN XY: 105478

Gnomad AFR exome AF: 0.573

Gnomad AMR exome AF: 0.775

Gnomad ASJ exome AF: 0.793

Gnomad EAS exome AF: 0.526

Gnomad SAS exome AF: 0.888

Gnomad FIN exome AF: 0.720

Gnomad NFE exome AF: 0.775

Gnomad OTH exome AF: 0.775

GnomAD4 exome AF: 0.770 AC: 1080904 AN: 1404190 Hom.: 418714 Cov.: 25 AF XY: 0.773 AC XY: 538485 AN XY: 696874

Gnomad4 AFR exome AF: 0.566

Gnomad4 AMR exome AF: 0.772

Gnomad4 ASJ exome AF: 0.796

Gnomad4 EAS exome AF: 0.584

Gnomad4 SAS exome AF: 0.882

Gnomad4 FIN exome AF: 0.722

Gnomad4 NFE exome AF: 0.775

Gnomad4 OTH exome AF: 0.765

GnomAD4 genome AF: 0.707 AC: 107536 AN: 152072 Hom.: 38897 Cov.: 32 AF XY: 0.707 AC XY: 52527 AN XY: 74322

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.759

Alfa AF: 0.745 Hom.: 7889

Bravo AF: 0.707

Asia WGS AF: 0.734 AC: 2549 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	0.92
DANN	Benign	0.30

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: rs1928104; hg19: chr13-99540395; COSMIC: COSV59622979;