9-121634032-C-G

Variant names:

• chr9-121634032-C-G
• rs555996
• NM_032552.4:c.41-44646C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032552.4(DAB2IP):​c.41-44646C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,080 control chromosomes in the GnomAD database, including 49,046 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 0.80 (49046 hom., cov: 31)
• Consequence: DAB2IP NM_032552.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 2 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAB2IP	NM_032552.4	c.41-44646C>G		intron_variant	Intron 1 of 16		NP_115941.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAB2IP	ENST00000259371.7	c.41-44646C>G		intron_variant	Intron 1 of 16	5		ENSP00000259371.2
DAB2IP	ENST00000489314.1	c.103+35406C>G		intron_variant	Intron 1 of 1	3		ENSP00000497730.1
DAB2IP	ENST00000436835.6	n.41-44646C>G		intron_variant	Intron 1 of 5	3		ENSP00000409327.2

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121340 AN: 151962 Hom.: 48996 Cov.: 31

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.777

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.799 AC: 121448 AN: 152080 Hom.: 49046 Cov.: 31 AF XY: 0.803 AC XY: 59713 AN XY: 74324

African (AFR) AF: 0.891 AC: 36980 AN: 41500

American (AMR) AF: 0.797 AC: 12183 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2578 AN: 3470

East Asian (EAS) AF: 0.946 AC: 4874 AN: 5152

South Asian (SAS) AF: 0.855 AC: 4106 AN: 4802

European-Finnish (FIN) AF: 0.805 AC: 8523 AN: 10594

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49585 AN: 67966

Other (OTH) AF: 0.775 AC: 1637 AN: 2112

Alfa AF: 0.726 Hom.: 2295

Bravo AF: 0.800

Asia WGS AF: 0.897 AC: 3119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.89
DANN	Benign	0.48
PhyloP100		-0.091
Mutation Taster		=100/0	polymorphism (auto)

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: rs555996; hg19: chr9-124396311;