rs2890080

chrX-118684873-C-AchrX-118684873-C-T

Variant summary

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

The NM_144658.4(DOCK11):c.6103-815C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 111,381 control chromosomes in the GnomAD database, including 1,016 homozygotes. There are 3,309 hemizygotes in GnomAD. 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 0.11 (1016 hom., 3309 hem., cov: 22)
• Consequence: DOCK11 NM_144658.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

Genes affected

DOCK11 (HGNC:23483): (dedicator of cytokinesis 11) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in several processes, including marginal zone B cell differentiation; positive regulation of GTPase activity; and positive regulation of filopodium assembly. Predicted to be located in cytosol. [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=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DOCK11	NM_144658.4	c.6103-815C>A		intron_variant		ENST00000276202.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOCK11	ENST00000276202.9	c.6103-815C>A		intron_variant		1	NM_144658.4	P4
DOCK11	ENST00000276204.10	c.6115-815C>A		intron_variant		5		A1
DOCK11	ENST00000632573.1	c.116-647C>A		intron_variant		2
DOCK11	ENST00000633080.1	c.5590-815C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.111 AC: 12334 AN: 111327 Hom.: 1016 Cov.: 22 AF XY: 0.0983 AC XY: 3299 AN XY: 33573

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0337

Gnomad AMR AF: 0.0517

Gnomad ASJ AF: 0.0558

Gnomad EAS AF: 0.000560

Gnomad SAS AF: 0.0192

Gnomad FIN AF: 0.0605

Gnomad MID AF: 0.0596

Gnomad NFE AF: 0.0493

Gnomad OTH AF: 0.0883

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.111 AC: 12345 AN: 111381 Hom.: 1016 Cov.: 22 AF XY: 0.0984 AC XY: 3309 AN XY: 33637

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.0516

Gnomad4 ASJ AF: 0.0558

Gnomad4 EAS AF: 0.000561

Gnomad4 SAS AF: 0.0185

Gnomad4 FIN AF: 0.0605

Gnomad4 NFE AF: 0.0493

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0818 Hom.: 447

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	9.0
Dann	Benign	0.81

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: rs2890080; hg19: chrX-117818836;