rs10818589

Variant names:

• chr9-121746971-C-T
• rs10818589
• NM_001395010.1:c.363-10042C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395010.1(DAB2IP):​c.363-10042C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 151,990 control chromosomes in the GnomAD database, including 1,912 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 0.14 (1912 hom., cov: 32)
• Consequence: DAB2IP NM_001395010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAB2IP	NM_001395010.1	c.363-10042C>T		intron_variant	Intron 3 of 15	ENST00000408936.8	NP_001381939.1
DAB2IP	NM_032552.4	c.279-10042C>T		intron_variant	Intron 3 of 16		NP_115941.2
DAB2IP	NM_138709.2	c.-11+4050C>T		intron_variant	Intron 1 of 13		NP_619723.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAB2IP	ENST00000408936.8	c.363-10042C>T		intron_variant	Intron 3 of 15	5	NM_001395010.1	ENSP00000386183.3

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20934 AN: 151870 Hom.: 1912 Cov.: 32

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.138 AC: 20924 AN: 151990 Hom.: 1912 Cov.: 32 AF XY: 0.139 AC XY: 10355 AN XY: 74276

Gnomad4 AFR AF: 0.0359

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.127

Alfa AF: 0.170 Hom.: 1791

Bravo AF: 0.134

Asia WGS AF: 0.264 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.34

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: rs10818589; hg19: chr9-124509250;