rs1984038

chr9-121661910-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAB2IP	NM_001395010.1	c.124+10011C>G		intron_variant		ENST00000408936.8
DAB2IP	NM_032552.4	c.41-16768C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAB2IP	ENST00000408936.8	c.124+10011C>G		intron_variant		5	NM_001395010.1	A1

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

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0617

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.246

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.37
Dann	Benign	0.25

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

Publications

LitVar

Other links and lift over

dbSNP: rs1984038; hg19: chr9-124424189;