rs200769141

Variant names:

• chr9-121699387-C-G
• rs200769141
• NM_001395010.1:c.291C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-121699387-C-G
• chr9-121699387-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 3 publications found

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]

ENSG00000293923 (HGNC:):

ACMG classification

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

Sel.	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.: 31

GnomAD2 exomes AF: 0.00000553 AC: 1 AN: 180762 AF XY: 0.00000976

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: 0 AN: 1330762 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 661970

African (AFR) AF: 0.00 AC: 0 AN: 27132

American (AMR) AF: 0.00 AC: 0 AN: 33624

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21598

East Asian (EAS) AF: 0.00 AC: 0 AN: 28488

South Asian (SAS) AF: 0.00 AC: 0 AN: 74746

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48086

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5200

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1039430

Other (OTH) AF: 0.00 AC: 0 AN: 52458

GnomAD4 genome Cov.: 31

ExAC AF: 0.00000842 AC: 1

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	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
M_CAP	Uncertain	0.23	D
MetaRNN	Benign	0.19	T
MetaSVM	Benign	-0.75	T
MutationAssessor	Benign	1.7	L
PhyloP100		-0.045
PrimateAI	Pathogenic	0.92	D
PROVEAN	Uncertain	-2.8	D
REVEL	Benign	0.092
Sift	Benign	0.69	T
Sift4G	Benign	0.067	T
Vest4		0.53
MutPred		0.17		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
Mutation Taster		=81/19	polymorphism

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

Other links and lift over

dbSNP: rs200769141; hg19: chr9-124461666;