chr9-121737701-G-A

Position:

• chr9-121737701-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001395010.1(DAB2IP):​c.363-19312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 985,438 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0031 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0034 (12 hom.)
• Consequence: DAB2IP NM_001395010.1 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.83

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 9-121737701-G-A is Benign according to our data. Variant chr9-121737701-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2659479.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 479 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAB2IP	NM_001395010.1	c.363-19312G>A		intron_variant		ENST00000408936.8
DAB2IP	NM_032552.4	c.279-19312G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAB2IP	ENST00000408936.8	c.363-19312G>A		intron_variant		5	NM_001395010.1	A1

Frequencies

GnomAD3 genomes AF: 0.00315 AC: 479 AN: 152210 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000627

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00249

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00494

Gnomad OTH AF: 0.00239

GnomAD4 exome AF: 0.00338 AC: 2820 AN: 833110 Hom.: 12 Cov.: 29 AF XY: 0.00343 AC XY: 1321 AN XY: 384714

Gnomad4 AFR exome AF: 0.000253

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0151

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00389

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00340

Gnomad4 OTH exome AF: 0.00308

GnomAD4 genome AF: 0.00314 AC: 479 AN: 152328 Hom.: 1 Cov.: 33 AF XY: 0.00305 AC XY: 227 AN XY: 74486

Gnomad4 AFR AF: 0.000625

Gnomad4 AMR AF: 0.00248

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00269

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00494

Gnomad4 OTH AF: 0.00237

Alfa AF: 0.00138 Hom.: 0

Bravo AF: 0.00297

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2024

DAB2IP: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.71
DANN	Benign	0.82

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: rs145251128; hg19: chr9-124499980;