rs10818583

Variant names:

• chr9-121659982-G-A
• rs10818583
• NM_001395010.1:c.124+8083G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-121659982-G-A
• chr9-121659982-G-C

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+8083G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,682 control chromosomes in the GnomAD database, including 3,675 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 0.20 (3675 hom., cov: 31)
• Consequence: DAB2IP NM_001395010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 9 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAB2IP	NM_001395010.1	MANE Select	c.124+8083G>A		intron	N/A	NP_001381939.1
	DAB2IP	NM_032552.4		c.41-18696G>A		intron	N/A	NP_115941.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAB2IP	ENST00000408936.8	TSL:5 MANE Select	c.124+8083G>A		intron	N/A	ENSP00000386183.3
	DAB2IP	ENST00000259371.7	TSL:5	c.41-18696G>A		intron	N/A	ENSP00000259371.2
	DAB2IP	ENST00000489314.1	TSL:3	c.104-18696G>A		intron	N/A	ENSP00000497730.1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30065 AN: 151564 Hom.: 3671 Cov.: 31

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.198 AC: 30080 AN: 151682 Hom.: 3675 Cov.: 31 AF XY: 0.200 AC XY: 14848 AN XY: 74078

African (AFR) AF: 0.0608 AC: 2518 AN: 41420

American (AMR) AF: 0.189 AC: 2887 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1470 AN: 5070

South Asian (SAS) AF: 0.314 AC: 1498 AN: 4776

European-Finnish (FIN) AF: 0.248 AC: 2601 AN: 10506

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17541 AN: 67876

Other (OTH) AF: 0.198 AC: 416 AN: 2102

Alfa AF: 0.160 Hom.: 430

Bravo AF: 0.188

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.81
DANN	Benign	0.44
PhyloP100		-0.63
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: rs10818583; hg19: chr9-124422261;