rs35061590

Positions:

• chr9-121713734-G-T

Variant summary

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

The NM_001395010.1(DAB2IP):​c.362+14276G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 152,256 control chromosomes in the GnomAD database, including 166 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 0.040 (166 hom., cov: 33)
• Consequence: DAB2IP NM_001395010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DAB2IP	NM_001395010.1	c.362+14276G>T		intron_variant		ENST00000408936.8	NP_001381939.1
DAB2IP	NM_032552.4	c.278+14276G>T		intron_variant			NP_115941.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAB2IP	ENST00000408936.8	c.362+14276G>T		intron_variant		5	NM_001395010.1	ENSP00000386183.3
DAB2IP	ENST00000259371.7	c.278+14276G>T		intron_variant		5		ENSP00000259371.2
DAB2IP	ENST00000699487.1	c.218+12621G>T		intron_variant				ENSP00000514398.1
DAB2IP	ENST00000436835.6	n.144+34953G>T		intron_variant		3		ENSP00000409327.2

Frequencies

GnomAD3 genomes AF: 0.0397 AC: 6039 AN: 152138 Hom.: 166 Cov.: 33

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0306

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0603

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0396 AC: 6036 AN: 152256 Hom.: 166 Cov.: 33 AF XY: 0.0379 AC XY: 2819 AN XY: 74444

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0317

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0178

Gnomad4 FIN AF: 0.0306

Gnomad4 NFE AF: 0.0603

Gnomad4 OTH AF: 0.0455

Alfa AF: 0.0455 Hom.: 42

Bravo AF: 0.0402

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.64

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: rs35061590; hg19: chr9-124476013;