rs200769141

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 š‘“: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

DAB2IP
NM_001395010.1 missense

Scores

2
4
13

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]

Genome browser will be placed here

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
DAB2IPNM_001395010.1 linkc.291C>G p.Asp97Glu missense_variant Exon 3 of 16 ENST00000408936.8 NP_001381939.1
DAB2IPNM_032552.4 linkc.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 Appris UniProt
DAB2IPENST00000408936.8 linkc.291C>G p.Asp97Glu missense_variant Exon 3 of 16 5 NM_001395010.1 ENSP00000386183.3 Q5VWQ8-1
DAB2IPENST00000259371.7 linkc.207C>G p.Asp69Glu missense_variant Exon 3 of 17 5 ENSP00000259371.2 Q5VWQ8-5
DAB2IPENST00000436835.6 linkn.144+20606C>G intron_variant Intron 2 of 5 3 ENSP00000409327.2 F6R503

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.00000553
AC:
1
AN:
180762
Hom.:
0
AF XY:
0.00000976
AC XY:
1
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:
0
AN:
1330762
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
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.:
31
ExAC
AF:
0.00000842
AC:
1

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
T
BayesDel_noAF
Benign
-0.40
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.22
.;.;T;.
Eigen
Benign
0.072
Eigen_PC
Benign
-0.0052
FATHMM_MKL
Benign
0.74
D
LIST_S2
Uncertain
0.93
D;D;D;D
M_CAP
Uncertain
0.23
D
MetaRNN
Benign
0.19
T;T;T;T
MetaSVM
Benign
-0.75
T
MutationAssessor
Benign
1.7
.;.;L;.
PrimateAI
Pathogenic
0.92
D
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
D
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.

Other links and lift over

dbSNP: rs200769141; hg19: chr9-124461666; API