rs3747851

Variant names:

• chr9-121758981-G-A
• rs3747851
• NM_001395010.1:c.600G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-121758981-G-A
• chr9-121758981-G-C
• chr9-121758981-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001395010.1(DAB2IP):​c.600G>A​(p.Ala200Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,612,336 control chromosomes in the GnomAD database, including 1,154 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 0.012 (92 hom., cov: 33)
  • Exomes 𝑓: 0.011 (1062 hom.)
• Consequence: DAB2IP NM_001395010.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.43
• Publications: 11 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP7: Synonymous conserved (PhyloP=-4.43 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395010.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAB2IP	NM_001395010.1	MANE Select	c.600G>A	p.Ala200Ala	synonymous	Exon 5 of 16	NP_001381939.1	Q5VWQ8-1
	DAB2IP	NM_032552.4		c.516G>A	p.Ala172Ala	synonymous	Exon 5 of 17	NP_115941.2	Q5VWQ8-5
	DAB2IP	NM_138709.2		c.228G>A	p.Ala76Ala	synonymous	Exon 3 of 14	NP_619723.1	Q5VWQ8-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAB2IP	ENST00000408936.8	TSL:5 MANE Select	c.600G>A	p.Ala200Ala	synonymous	Exon 5 of 16	ENSP00000386183.3	Q5VWQ8-1
	DAB2IP	ENST00000309989.1	TSL:1	c.228G>A	p.Ala76Ala	synonymous	Exon 3 of 14	ENSP00000310827.1	Q5VWQ8-2
	DAB2IP	ENST00000259371.7	TSL:5	c.516G>A	p.Ala172Ala	synonymous	Exon 5 of 17	ENSP00000259371.2	Q5VWQ8-5

Frequencies

GnomAD3 genomes AF: 0.0115 AC: 1753 AN: 152136 Hom.: 91 Cov.: 33

Gnomad AFR AF: 0.00232

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0328

Gnomad FIN AF: 0.0187

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00112

Gnomad OTH AF: 0.0167

GnomAD2 exomes AF: 0.0282 AC: 6976 AN: 247104 AF XY: 0.0262

Gnomad AFR exome AF: 0.00171

Gnomad AMR exome AF: 0.0754

Gnomad ASJ exome AF: 0.000201

Gnomad EAS exome AF: 0.155

Gnomad FIN exome AF: 0.0184

Gnomad NFE exome AF: 0.00105

Gnomad OTH exome AF: 0.0180

GnomAD4 exome AF: 0.0109 AC: 15859 AN: 1460082 Hom.: 1062 Cov.: 31 AF XY: 0.0112 AC XY: 8141 AN XY: 726032

African (AFR) AF: 0.00117 AC: 39 AN: 33468

American (AMR) AF: 0.0694 AC: 3085 AN: 44458

Ashkenazi Jewish (ASJ) AF: 0.000230 AC: 6 AN: 26078

East Asian (EAS) AF: 0.192 AC: 7600 AN: 39650

South Asian (SAS) AF: 0.0321 AC: 2743 AN: 85414

European-Finnish (FIN) AF: 0.0201 AC: 1069 AN: 53308

Middle Eastern (MID) AF: 0.00208 AC: 12 AN: 5764

European-Non Finnish (NFE) AF: 0.000423 AC: 470 AN: 1111598

Other (OTH) AF: 0.0138 AC: 835 AN: 60344

GnomAD4 genome AF: 0.0115 AC: 1753 AN: 152254 Hom.: 92 Cov.: 33 AF XY: 0.0134 AC XY: 1000 AN XY: 74428

African (AFR) AF: 0.00231 AC: 96 AN: 41554

American (AMR) AF: 0.0228 AC: 349 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3472

East Asian (EAS) AF: 0.163 AC: 843 AN: 5170

South Asian (SAS) AF: 0.0324 AC: 156 AN: 4814

European-Finnish (FIN) AF: 0.0187 AC: 198 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00112 AC: 76 AN: 68008

Other (OTH) AF: 0.0156 AC: 33 AN: 2114

Alfa AF: 0.00662 Hom.: 85

Bravo AF: 0.0133

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.13
DANN	Benign	0.75
PhyloP100		-4.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
Splicevardb		2.0
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: rs3747851; hg19: chr9-124521260; COSMIC: COSV52260158; COSMIC: COSV52260158;