9-121609873-C-T

Variant names:

• chr9-121609873-C-T
• rs10985332
• NM_032552.4:c.40+42645C>T

Variant summary

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

The NM_032552.4(DAB2IP):​c.40+42645C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,092 control chromosomes in the GnomAD database, including 5,911 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 0.26 (5911 hom., cov: 33)
• Consequence: DAB2IP NM_032552.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 1 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAB2IP	NM_032552.4	c.40+42645C>T		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.40+42645C>T		intron_variant	Intron 1 of 16	5		ENSP00000259371.2
DAB2IP	ENST00000489314.1	c.103+11247C>T		intron_variant	Intron 1 of 1	3		ENSP00000497730.1
DAB2IP	ENST00000436835.6	n.40+42645C>T		intron_variant	Intron 1 of 5	3		ENSP00000409327.2

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39376 AN: 151974 Hom.: 5912 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.259 AC: 39386 AN: 152092 Hom.: 5911 Cov.: 33 AF XY: 0.266 AC XY: 19808 AN XY: 74358

African (AFR) AF: 0.269 AC: 11148 AN: 41500

American (AMR) AF: 0.388 AC: 5935 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3472

East Asian (EAS) AF: 0.582 AC: 2999 AN: 5150

South Asian (SAS) AF: 0.343 AC: 1652 AN: 4812

European-Finnish (FIN) AF: 0.243 AC: 2574 AN: 10588

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13670 AN: 67976

Other (OTH) AF: 0.257 AC: 542 AN: 2110

Alfa AF: 0.227 Hom.: 7797

Bravo AF: 0.272

Asia WGS AF: 0.467 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.40
PhyloP100		1.0
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: rs10985332; hg19: chr9-124372152;