9-121617509-C-T

Variant names:

• chr9-121617509-C-T
• rs1984035
• NM_032552.4:c.40+50281C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032552.4(DAB2IP):​c.40+50281C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,016 control chromosomes in the GnomAD database, including 18,605 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 0.48 (18605 hom., cov: 32)
• Consequence: DAB2IP NM_032552.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAB2IP	NM_032552.4	c.40+50281C>T		intron_variant	Intron 1 of 16		NP_115941.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAB2IP	ENST00000259371.7	c.40+50281C>T		intron_variant	Intron 1 of 16	5		ENSP00000259371.2
DAB2IP	ENST00000489314.1	c.103+18883C>T		intron_variant	Intron 1 of 1	3		ENSP00000497730.1
DAB2IP	ENST00000436835.6	n.40+50281C>T		intron_variant	Intron 1 of 5	3		ENSP00000409327.2

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72562 AN: 151898 Hom.: 18597 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.478 AC: 72596 AN: 152016 Hom.: 18605 Cov.: 32 AF XY: 0.489 AC XY: 36326 AN XY: 74308

African (AFR) AF: 0.528 AC: 21878 AN: 41456

American (AMR) AF: 0.561 AC: 8575 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3472

East Asian (EAS) AF: 0.970 AC: 5007 AN: 5164

South Asian (SAS) AF: 0.622 AC: 2995 AN: 4816

European-Finnish (FIN) AF: 0.463 AC: 4885 AN: 10558

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26512 AN: 67962

Other (OTH) AF: 0.466 AC: 985 AN: 2114

Alfa AF: 0.420 Hom.: 23394

Bravo AF: 0.489

Asia WGS AF: 0.771 AC: 2683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.72
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1984035; hg19: chr9-124379788;