9-121631045-C-T

Variant names:

• chr9-121631045-C-T
• rs2243421
• NM_032552.4:c.41-47633C>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.41-47633C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 152,076 control chromosomes in the GnomAD database, including 18,385 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 0.43 (18385 hom., cov: 33)
• Consequence: DAB2IP NM_032552.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAB2IP	NM_032552.4	c.41-47633C>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.41-47633C>T		intron_variant	Intron 1 of 16	5		ENSP00000259371.2
DAB2IP	ENST00000489314.1	c.103+32419C>T		intron_variant	Intron 1 of 1	3		ENSP00000497730.1
DAB2IP	ENST00000436835.6	n.41-47633C>T		intron_variant	Intron 1 of 5	3		ENSP00000409327.2

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65890 AN: 151956 Hom.: 18346 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.434 AC: 65982 AN: 152076 Hom.: 18385 Cov.: 33 AF XY: 0.437 AC XY: 32498 AN XY: 74336

African (AFR) AF: 0.767 AC: 31848 AN: 41520

American (AMR) AF: 0.464 AC: 7094 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3470

East Asian (EAS) AF: 0.640 AC: 3298 AN: 5152

South Asian (SAS) AF: 0.388 AC: 1865 AN: 4812

European-Finnish (FIN) AF: 0.302 AC: 3198 AN: 10572

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16805 AN: 67944

Other (OTH) AF: 0.389 AC: 822 AN: 2112

Alfa AF: 0.359 Hom.: 1592

Bravo AF: 0.462

Asia WGS AF: 0.529 AC: 1843 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.53
PhyloP100		-0.25
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: rs2243421; hg19: chr9-124393324;