rs7025486

Variant names:

• chr9-121660124-G-A
• rs7025486
• NM_001395010.1:c.124+8225G>A

Variant summary

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

The NM_001395010.1(DAB2IP):​c.124+8225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,920 control chromosomes in the GnomAD database, including 5,912 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 (5912 hom., cov: 32)
• Consequence: DAB2IP NM_001395010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 74 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAB2IP	NM_001395010.1	c.124+8225G>A		intron_variant	Intron 1 of 15	ENST00000408936.8	NP_001381939.1
DAB2IP	NM_032552.4	c.41-18554G>A		intron_variant	Intron 1 of 16		NP_115941.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAB2IP	ENST00000408936.8	c.124+8225G>A		intron_variant	Intron 1 of 15	5	NM_001395010.1	ENSP00000386183.3

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41577 AN: 151802 Hom.: 5907 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.274 AC: 41620 AN: 151920 Hom.: 5912 Cov.: 32 AF XY: 0.273 AC XY: 20273 AN XY: 74226

African (AFR) AF: 0.321 AC: 13305 AN: 41438

American (AMR) AF: 0.213 AC: 3254 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3466

East Asian (EAS) AF: 0.293 AC: 1491 AN: 5096

South Asian (SAS) AF: 0.313 AC: 1506 AN: 4812

European-Finnish (FIN) AF: 0.249 AC: 2629 AN: 10564

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17671 AN: 67946

Other (OTH) AF: 0.252 AC: 532 AN: 2112

Alfa AF: 0.265 Hom.: 20533

Bravo AF: 0.273

Asia WGS AF: 0.293 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.59
PhyloP100		0.41
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: rs7025486; hg19: chr9-124422403;