Genetic Variant DAB2IP:p.Asp97Glu (chr9-121699387-C-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001395010.1(DAB2IP):c.291C>G(p.Asp97Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. D97D) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

DAB2IP
NM_001395010.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0450

Publications

3 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:

ENSG00000293923 (HGNC:):

ENSG00000293923 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.186248).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395010.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAB2IP	NM_001395010.1	MANE Select	c.291C>G	p.Asp97Glu	missense	Exon 3 of 16	NP_001381939.1	Q5VWQ8-1
	DAB2IP	NM_032552.4		c.207C>G	p.Asp69Glu	missense	Exon 3 of 17	NP_115941.2	Q5VWQ8-5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
DAB2IP	ENST00000408936.8	TSL:5 MANE Select	c.291C>G	p.Asp97Glu	missense	Exon 3 of 16	ENSP00000386183.3	Q5VWQ8-1
DAB2IP	ENST00000259371.7	TSL:5	c.207C>G	p.Asp69Glu	missense	Exon 3 of 17	ENSP00000259371.2	Q5VWQ8-5
DAB2IP	ENST00000436835.6	TSL:3	n.144+20606C>G		intron	N/A	ENSP00000409327.2	F6R503

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000553

AC:

AN:

180762

AF XY:

0.00000976

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1330762

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

661970

African (AFR)

AF:

0.00

AC:

AN:

27132

American (AMR)

AF:

0.00

AC:

AN:

33624

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21598

East Asian (EAS)

AF:

0.00

AC:

AN:

28488

South Asian (SAS)

AF:

0.00

AC:

AN:

74746

European-Finnish (FIN)

AF:

0.00

AC:

AN:

48086

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5200

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1039430

Other (OTH)

AF:

0.00

AC:

AN:

52458

GnomAD4 genome

Cov.:

ExAC

AF:

0.00000842

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.60

BayesDel_addAF

Benign

-0.20

BayesDel_noAF

Benign

-0.40

CADD

Uncertain

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.22

Eigen

Benign

0.072

Eigen_PC

Benign

-0.0052

FATHMM_MKL

Benign

0.74

LIST_S2

Uncertain

0.93

M_CAP

Uncertain

0.23

MetaRNN

Benign

0.19

MetaSVM

Benign

-0.75

MutationAssessor

Benign

1.7

PhyloP100

-0.045

PrimateAI

Pathogenic

0.92

PROVEAN

Uncertain

-2.8

REVEL

Benign

0.092

Sift

Benign

0.69

Sift4G

Benign

0.067

Vest4

0.53

MutPred

0.17

Gain of methylation at K67 (P = 0.0854)

MVP

0.69

MPC

0.90

ClinPred

0.83

GERP RS

2.2

Varity_R

0.36

gMVP

0.26

Mutation Taster

=81/19

polymorphism

(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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over