rs1984038

Variant names:

• chr9-121661910-C-G
• rs1984038
• NM_001395010.1:c.124+10011C>G

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+10011C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,536 control chromosomes in the GnomAD database, including 6,327 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 0.28 (6327 hom., cov: 31)
• Consequence: DAB2IP NM_001395010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• 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=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 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+10011C>G		intron	N/A	NP_001381939.1
	DAB2IP	NM_032552.4		c.41-16768C>G		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+10011C>G		intron	N/A	ENSP00000386183.3
	DAB2IP	ENST00000259371.7	TSL:5	c.41-16768C>G		intron	N/A	ENSP00000259371.2
	DAB2IP	ENST00000489314.1	TSL:3	c.104-16768C>G		intron	N/A	ENSP00000497730.1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42021 AN: 151420 Hom.: 6307 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.278 AC: 42082 AN: 151536 Hom.: 6327 Cov.: 31 AF XY: 0.273 AC XY: 20205 AN XY: 74026

African (AFR) AF: 0.376 AC: 15481 AN: 41194

American (AMR) AF: 0.214 AC: 3265 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3470

East Asian (EAS) AF: 0.0617 AC: 318 AN: 5156

South Asian (SAS) AF: 0.155 AC: 743 AN: 4792

European-Finnish (FIN) AF: 0.298 AC: 3130 AN: 10492

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17650 AN: 67900

Other (OTH) AF: 0.246 AC: 517 AN: 2098

Alfa AF: 0.279 Hom.: 789

Bravo AF: 0.273

Asia WGS AF: 0.139 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.37
DANN	Benign	0.25
PhyloP100		-1.6
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: rs1984038; hg19: chr9-124424189;