dbSNP rs1051039: DOCK1:c.*912G>C (chr10-127452339-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001290223.2(DOCK1):c.*912G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,168 control chromosomes in the GnomAD database, including 16,455 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 0.45 ( 16415 hom., cov: 31)

Exomes 𝑓: 0.45 ( 40 hom. )

Consequence

DOCK1
NM_001290223.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0750

Publications

6 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DOCK1	NM_001290223.2 link	c.*912G>C		3_prime_UTR_variant	Exon 52 of 52	ENST00000623213.2	NP_001277152.2	B2RUU3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DOCK1	ENST00000623213.2 link	c.*912G>C		3_prime_UTR_variant	Exon 52 of 52	1	NM_001290223.2	ENSP00000485033.1		A0A096LNH6
DOCK1	ENST00000280333.9 link	c.*912G>C		3_prime_UTR_variant	Exon 52 of 52	1		ENSP00000280333.6		Q14185

Frequencies

GnomAD3 genomes

AF:

0.450

AC:

67770

AN:

150618

Hom.:

16403

Cov.:

show subpopulations

Gnomad AFR

AF:

0.255

Gnomad AMI

AF:

0.488

Gnomad AMR

AF:

0.546

Gnomad ASJ

AF:

0.515

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.515

Gnomad FIN

AF:

0.455

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.540

Gnomad OTH

AF:

0.468

GnomAD4 exome

AF:

0.454

AC:

197

AN:

434

Hom.:

Cov.:

AF XY:

0.469

AC XY:

123

AN XY:

262

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.451

AC:

193

AN:

428

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.450

AC:

67813

AN:

150734

Hom.:

16415

Cov.:

AF XY:

0.448

AC XY:

32928

AN XY:

73514

show subpopulations

African (AFR)

AF:

0.254

AC:

10402

AN:

40896

American (AMR)

AF:

0.546

AC:

8311

AN:

15212

Ashkenazi Jewish (ASJ)

AF:

0.515

AC:

1783

AN:

3460

East Asian (EAS)

AF:

0.388

AC:

1983

AN:

5114

South Asian (SAS)

AF:

0.517

AC:

2465

AN:

4772

European-Finnish (FIN)

AF:

0.455

AC:

4661

AN:

10244

Middle Eastern (MID)

AF:

0.588

AC:

173

AN:

294

European-Non Finnish (NFE)

AF:

0.540

AC:

36599

AN:

67730

Other (OTH)

AF:

0.472

AC:

992

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

1697

3393

5090

6786

8483

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.474

Hom.:

2172

Bravo

AF:

0.441

Asia WGS

AF:

0.451

AC:

1564

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.7

(source)

DANN

Benign

0.64

PhyloP100

0.075

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs1051039

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over