Genetic Variant DOCK2:p.Tyr122Tyr (chr5-169674341-C-T) – ACMG Classification: Benign (-15 pts)

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_004946.3(DOCK2):c.366C>T(p.Tyr122Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00303 in 1,614,094 control chromosomes in the GnomAD database, including 121 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 63 hom., cov: 32)

Exomes 𝑓: 0.0018 ( 58 hom. )

Consequence

DOCK2
NM_004946.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.38

Variant links:

Genes affected

DOCK2 (HGNC:2988): (dedicator of cytokinesis 2) The protein encoded by this gene belongs to the CDM protein family. It is specifically expressed in hematopoietic cells and is predominantly expressed in peripheral blood leukocytes. The protein is involved in remodeling of the actin cytoskeleton required for lymphocyte migration in response to chemokine signaling. It activates members of the Rho family of GTPases, for example RAC1 and RAC2, by acting as a guanine nucleotide exchange factor (GEF) to exchange bound GDP for free GTP. Mutations in this gene result in immunodeficiency 40 (IMD40), a combined form of immunodeficiency that affects T cell number and function, also with variable defects in B cell and NK cell function. [provided by RefSeq, May 2018]

DOCK2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 5-169674341-C-T is Benign according to our data. Variant chr5-169674341-C-T is described in ClinVar as [Benign]. Clinvar id is 476011.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.38 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DOCK2	NM_004946.3 link	c.366C>T	p.Tyr122Tyr	synonymous_variant	Exon 6 of 52	ENST00000520908.7	NP_004937.1	Q92608-1Q5XG91

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
DOCK2	ENST00000520908.7 link	c.366C>T	p.Tyr122Tyr	synonymous_variant	Exon 6 of 52	2	NM_004946.3	ENSP00000429283.3	Q92608-1
DOCK2	ENST00000524185.5 link	n.366C>T		non_coding_transcript_exon_variant	Exon 6 of 53	1		ENSP00000428850.1	E5RFJ0
DOCK2	ENST00000519628.2 link	c.366C>T	p.Tyr122Tyr	synonymous_variant	Exon 6 of 28	3		ENSP00000428841.2	H0YB76
DOCK2	ENST00000522138.2 link	n.366C>T		non_coding_transcript_exon_variant	Exon 6 of 52	3		ENSP00000512484.1	A0A8Q3WL64

Frequencies

GnomAD3 genomes

AF:

0.0147

AC:

2237

AN:

152134

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0500

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00635

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.000772

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000485

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.00411

AC:

1031

AN:

251142

Hom.:

AF XY:

0.00301

AC XY:

408

AN XY:

135708

show subpopulations

Gnomad AFR exome

AF:

0.0507

Gnomad AMR exome

AF:

0.00312

Gnomad ASJ exome

AF:

0.00288

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.000359

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.000388

Gnomad OTH exome

AF:

0.00180

GnomAD4 exome

AF:

0.00181

AC:

2640

AN:

1461842

Hom.:

Cov.:

AF XY:

0.00160

AC XY:

1164

AN XY:

727214

show subpopulations

Gnomad4 AFR exome

AF:

0.0527

Gnomad4 AMR exome

AF:

0.00364

Gnomad4 ASJ exome

AF:

0.00287

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.000255

Gnomad4 FIN exome

AF:

0.0000374

Gnomad4 NFE exome

AF:

0.000309

Gnomad4 OTH exome

AF:

0.00394

GnomAD4 genome

AF:

0.0148

AC:

2248

AN:

152252

Hom.:

Cov.:

AF XY:

0.0137

AC XY:

1018

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0501

Gnomad4 AMR

AF:

0.00640

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000485

Gnomad4 OTH

AF:

0.0128

Alfa

AF:

0.00686

Hom.:

Bravo

AF:

0.0168

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.000273

EpiControl

AF:

0.000474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

DOCK2 deficiency

Benign:1

Jan 28, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

2.8

DANN

Benign

0.51

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over