dbSNP rs3747851: DAB2IP:p.Ala200Ala (chr9-121758981-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001395010.1(DAB2IP):c.600G>A(p.Ala200Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,612,336 control chromosomes in the GnomAD database, including 1,154 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 0.012 ( 92 hom., cov: 33)

Exomes 𝑓: 0.011 ( 1062 hom. )

Consequence

DAB2IP
NM_001395010.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.43

Publications

11 publications found

Variant links:

Genes affected

DAB2IP (HGNC:17294): (DAB2 interacting protein) DAB2IP is a Ras (MIM 190020) GTPase-activating protein (GAP) that acts as a tumor suppressor. The DAB2IP gene is inactivated by methylation in prostate and breast cancers (Yano et al., 2005 [PubMed 15386433]).[supplied by OMIM, May 2010]

DAB2IP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP7

Synonymous conserved (PhyloP=-4.43 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAB2IP	NM_001395010.1 link	c.600G>A	p.Ala200Ala	synonymous_variant	Exon 5 of 16	ENST00000408936.8	NP_001381939.1
DAB2IP	NM_032552.4 link	c.516G>A	p.Ala172Ala	synonymous_variant	Exon 5 of 17		NP_115941.2	Q5VWQ8-5
DAB2IP	NM_138709.2 link	c.228G>A	p.Ala76Ala	synonymous_variant	Exon 3 of 14		NP_619723.1	Q5VWQ8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAB2IP	ENST00000408936.8 link	c.600G>A	p.Ala200Ala	synonymous_variant	Exon 5 of 16	5	NM_001395010.1	ENSP00000386183.3		Q5VWQ8-1

Frequencies

GnomAD3 genomes

AF:

0.0115

AC:

1753

AN:

152136

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00232

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0225

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.0328

Gnomad FIN

AF:

0.0187

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00112

Gnomad OTH

AF:

0.0167

GnomAD2 exomes

AF:

0.0282

AC:

6976

AN:

247104

AF XY:

0.0262

show subpopulations

Gnomad AFR exome

AF:

0.00171

Gnomad AMR exome

AF:

0.0754

Gnomad ASJ exome

AF:

0.000201

Gnomad EAS exome

AF:

0.155

Gnomad FIN exome

AF:

0.0184

Gnomad NFE exome

AF:

0.00105

Gnomad OTH exome

AF:

0.0180

GnomAD4 exome

AF:

0.0109

AC:

15859

AN:

1460082

Hom.:

1062

Cov.:

AF XY:

0.0112

AC XY:

8141

AN XY:

726032

show subpopulations

African (AFR)

AF:

0.00117

AC:

AN:

33468

American (AMR)

AF:

0.0694

AC:

3085

AN:

44458

Ashkenazi Jewish (ASJ)

AF:

0.000230

AC:

AN:

26078

East Asian (EAS)

AF:

0.192

AC:

7600

AN:

39650

South Asian (SAS)

AF:

0.0321

AC:

2743

AN:

85414

European-Finnish (FIN)

AF:

0.0201

AC:

1069

AN:

53308

Middle Eastern (MID)

AF:

0.00208

AC:

AN:

5764

European-Non Finnish (NFE)

AF:

0.000423

AC:

470

AN:

1111598

Other (OTH)

AF:

0.0138

AC:

835

AN:

60344

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

742

1484

2226

2968

3710

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

194

388

582

776

970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0115

AC:

1753

AN:

152254

Hom.:

Cov.:

AF XY:

0.0134

AC XY:

1000

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.00231

AC:

AN:

41554

American (AMR)

AF:

0.0228

AC:

349

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.000576

AC:

AN:

3472

East Asian (EAS)

AF:

0.163

AC:

843

AN:

5170

South Asian (SAS)

AF:

0.0324

AC:

156

AN:

4814

European-Finnish (FIN)

AF:

0.0187

AC:

198

AN:

10610

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00112

AC:

AN:

68008

Other (OTH)

AF:

0.0156

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

173

259

346

432

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00662

Hom.:

Bravo

AF:

0.0133

Asia WGS

AF:

0.0840

AC:

292

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.13

(source)

DANN

Benign

0.75

PhyloP100

-4.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

Splicevardb

2.0

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over