Variant rs2498947 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001290223.2(DOCK1):c.3044+14892G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,100 control chromosomes in the GnomAD database, including 7,110 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 0.27 ( 7109 hom., cov: 33)

Exomes 𝑓: 1.0 ( 1 hom. )

Consequence

DOCK1
NM_001290223.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33

Variant links:

Genes affected

DOCK1 (HGNC:2987): (dedicator of cytokinesis 1) This gene encodes a member of the dedicator of cytokinesis protein family. Dedicator of cytokinesis proteins act as guanine nucleotide exchange factors for small Rho family G proteins. The encoded protein regulates the small GTPase Rac, thereby influencing several biological processes, including phagocytosis and cell migration. Overexpression of this gene has also been associated with certain cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

DOCK1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DOCK1	NM_001290223.2 linkuse as main transcript	c.3044+14892G>A		intron_variant		ENST00000623213.2	NP_001277152.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
DOCK1	ENST00000623213.2 linkuse as main transcript	c.3044+14892G>A	intron_variant	1	NM_001290223.2	ENSP00000485033
DOCK1	ENST00000280333.9 linkuse as main transcript	c.2981+14892G>A	intron_variant	1		ENSP00000280333	P1
DOCK1	ENST00000484400.5 linkuse as main transcript	n.197+14892G>A	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41621

AN:

151980

Hom.:

7112

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0695

Gnomad AMI

AF:

0.407

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.411

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.517

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.356

Gnomad OTH

AF:

0.308

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

1.00

GnomAD4 genome

AF:

0.274

AC:

41618

AN:

152098

Hom.:

7109

Cov.:

AF XY:

0.277

AC XY:

20592

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.0694

Gnomad4 AMR

AF:

0.337

Gnomad4 ASJ

AF:

0.411

Gnomad4 EAS

AF:

0.232

Gnomad4 SAS

AF:

0.518

Gnomad4 FIN

AF:

0.294

Gnomad4 NFE

AF:

0.356

Gnomad4 OTH

AF:

0.307

Alfa

AF:

0.329

Hom.:

4442

Bravo

AF:

0.267

Asia WGS

AF:

0.309

AC:

1077

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.3

DANN

Benign

0.71

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