chr9-121659982-G-A

Position:

• chr9-121659982-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAB2IP	NM_001395010.1	c.124+8083G>A		intron_variant		ENST00000408936.8
DAB2IP	NM_032552.4	c.41-18696G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAB2IP	ENST00000408936.8	c.124+8083G>A		intron_variant		5	NM_001395010.1	A1

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

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.198

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.81
DANN	Benign	0.44

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: rs10818583; hg19: chr9-124422261;