9-121592547-T-C

Variant names:

• chr9-121592547-T-C
• rs10513376
• NM_032552.4:c.40+25319T>C

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+25319T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,090 control chromosomes in the GnomAD database, including 6,057 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 0.27 (6057 hom., cov: 32)
• Consequence: DAB2IP NM_032552.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032552.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAB2IP	NM_032552.4		c.40+25319T>C		intron	N/A	NP_115941.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAB2IP	ENST00000259371.7	TSL:5	c.40+25319T>C		intron	N/A	ENSP00000259371.2
	DAB2IP	ENST00000436835.6	TSL:3	n.40+25319T>C		intron	N/A	ENSP00000409327.2

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41069 AN: 151970 Hom.: 6053 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.270 AC: 41095 AN: 152090 Hom.: 6057 Cov.: 32 AF XY: 0.261 AC XY: 19436 AN XY: 74358

African (AFR) AF: 0.261 AC: 10815 AN: 41468

American (AMR) AF: 0.232 AC: 3542 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3468

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5182

South Asian (SAS) AF: 0.0969 AC: 467 AN: 4818

European-Finnish (FIN) AF: 0.241 AC: 2548 AN: 10578

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21533 AN: 67988

Other (OTH) AF: 0.291 AC: 613 AN: 2110

Alfa AF: 0.305 Hom.: 9659

Bravo AF: 0.271

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.30
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: rs10513376; hg19: chr9-124354826; COSMIC: COSV52256422;