dbSNP rs200769141: DAB2IP:p.Asp97Glu (chr9-121699387-C-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 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

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:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAB2IP	NM_001395010.1 link	c.291C>G	p.Asp97Glu	missense_variant	Exon 3 of 16	ENST00000408936.8	NP_001381939.1
DAB2IP	NM_032552.4 link	c.207C>G	p.Asp69Glu	missense_variant	Exon 3 of 17		NP_115941.2	Q5VWQ8-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
DAB2IP	ENST00000408936.8 link	c.291C>G	p.Asp97Glu	missense_variant	Exon 3 of 16	5	NM_001395010.1	ENSP00000386183.3	Q5VWQ8-1
DAB2IP	ENST00000259371.7 link	c.207C>G	p.Asp69Glu	missense_variant	Exon 3 of 17	5		ENSP00000259371.2	Q5VWQ8-5
DAB2IP	ENST00000436835.6 link	n.144+20606C>G		intron_variant	Intron 2 of 5	3		ENSP00000409327.2	F6R503

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000553

AC:

AN:

180762

Hom.:

AF XY:

0.00000976

AC XY:

AN XY:

102438

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 SAS exome

AF:

0.0000410

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

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ExAC

AF:

0.00000842

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.60

BayesDel_addAF

Benign

-0.20

BayesDel_noAF

Benign

-0.40

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.22

.;.;T;.

Eigen

Benign

0.072

Eigen_PC

Benign

-0.0052

FATHMM_MKL

Benign

0.74

LIST_S2

Uncertain

0.93

D;D;D;D

M_CAP

Uncertain

0.23

MetaRNN

Benign

0.19

T;T;T;T

MetaSVM

Benign

-0.75

MutationAssessor

Benign

1.7

.;.;L;.

PrimateAI

Pathogenic

0.92

PROVEAN

Uncertain

-2.8

D;D;N;N

REVEL

Benign

0.092

Sift

Benign

0.69

T;T;T;D

Sift4G

Benign

0.067

T;D;D;D

Vest4

0.53, 0.53

MutPred

0.17

Gain of methylation at K67 (P = 0.0854);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

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