9-121725216-C-T

Variant names:

• chr9-121725216-C-T
• rs13290547
• NM_001395010.1:c.362+25758C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001395010.1(DAB2IP):​c.362+25758C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0403 in 152,234 control chromosomes in the GnomAD database, including 167 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 (167 hom., cov: 32)
• Consequence: DAB2IP NM_001395010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 12 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAB2IP	NM_001395010.1	c.362+25758C>T		intron_variant	Intron 3 of 15	ENST00000408936.8	NP_001381939.1
DAB2IP	NM_032552.4	c.278+25758C>T		intron_variant	Intron 3 of 16		NP_115941.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAB2IP	ENST00000408936.8	c.362+25758C>T		intron_variant	Intron 3 of 15	5	NM_001395010.1	ENSP00000386183.3
DAB2IP	ENST00000259371.7	c.278+25758C>T		intron_variant	Intron 3 of 16	5		ENSP00000259371.2
DAB2IP	ENST00000699487.1	c.218+24103C>T		intron_variant	Intron 1 of 6			ENSP00000514398.1
DAB2IP	ENST00000436835.6	n.145-31797C>T		intron_variant	Intron 2 of 5	3		ENSP00000409327.2

Frequencies

GnomAD3 genomes AF: 0.0403 AC: 6134 AN: 152116 Hom.: 165 Cov.: 32

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0600

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0403 AC: 6138 AN: 152234 Hom.: 167 Cov.: 32 AF XY: 0.0386 AC XY: 2875 AN XY: 74416

African (AFR) AF: 0.0114 AC: 472 AN: 41538

American (AMR) AF: 0.0320 AC: 489 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3472

East Asian (EAS) AF: 0.0201 AC: 104 AN: 5178

South Asian (SAS) AF: 0.0178 AC: 86 AN: 4822

European-Finnish (FIN) AF: 0.0309 AC: 328 AN: 10606

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0600 AC: 4079 AN: 68008

Other (OTH) AF: 0.0502 AC: 106 AN: 2110

Alfa AF: 0.0546 Hom.: 828

Bravo AF: 0.0408

Asia WGS AF: 0.0250 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	14
DANN	Benign	0.87
PhyloP100		-0.33
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: rs13290547; hg19: chr9-124487495;