chr9-121699387-C-T

Variant names:

• chr9-121699387-C-T
• rs200769141
• NM_001395010.1:c.291C>T

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_Strong BP6_Very_Strong BP7 BS2

The NM_001395010.1(DAB2IP):​c.291C>T​(p.Asp97Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00341 in 1,480,430 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0031 (1 hom., cov: 31)
  • Exomes 𝑓: 0.0035 (19 hom.)
• Consequence: DAB2IP NM_001395010.1 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0450
• 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]

ENSG00000293923 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -17 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BP6: Variant 9-121699387-C-T is Benign according to our data. Variant chr9-121699387-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 781934.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.045 with no splicing effect.
• BS2: High AC in GnomAd4 at 462 AD gene.

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.291C>T	p.Asp97Asp	synonymous	Exon 3 of 16	NP_001381939.1	Q5VWQ8-1
	DAB2IP	NM_032552.4		c.207C>T	p.Asp69Asp	synonymous	Exon 3 of 17	NP_115941.2	Q5VWQ8-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAB2IP	ENST00000408936.8	TSL:5 MANE Select	c.291C>T	p.Asp97Asp	synonymous	Exon 3 of 16	ENSP00000386183.3	Q5VWQ8-1
	DAB2IP	ENST00000259371.7	TSL:5	c.207C>T	p.Asp69Asp	synonymous	Exon 3 of 17	ENSP00000259371.2	Q5VWQ8-5
	DAB2IP	ENST00000436835.6	TSL:3	n.144+20606C>T		intron	N/A	ENSP00000409327.2	F6R503

Frequencies

GnomAD3 genomes AF: 0.00308 AC: 461 AN: 149592 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000681

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00239

Gnomad ASJ AF: 0.0134

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.00333

Gnomad FIN AF: 0.000922

Gnomad MID AF: 0.00321

Gnomad NFE AF: 0.00476

Gnomad OTH AF: 0.00243

GnomAD2 exomes AF: 0.00328 AC: 593 AN: 180762 AF XY: 0.00323

Gnomad AFR exome AF: 0.000243

Gnomad AMR exome AF: 0.000605

Gnomad ASJ exome AF: 0.0123

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00218

Gnomad NFE exome AF: 0.00416

Gnomad OTH exome AF: 0.00385

GnomAD4 exome AF: 0.00345 AC: 4593 AN: 1330736 Hom.: 19 Cov.: 33 AF XY: 0.00346 AC XY: 2288 AN XY: 661960

African (AFR) AF: 0.000405 AC: 11 AN: 27132

American (AMR) AF: 0.00107 AC: 36 AN: 33624

Ashkenazi Jewish (ASJ) AF: 0.0138 AC: 299 AN: 21594

East Asian (EAS) AF: 0.00 AC: 0 AN: 28488

South Asian (SAS) AF: 0.00340 AC: 254 AN: 74742

European-Finnish (FIN) AF: 0.00252 AC: 121 AN: 48082

Middle Eastern (MID) AF: 0.000385 AC: 2 AN: 5200

European-Non Finnish (NFE) AF: 0.00356 AC: 3696 AN: 1039418

Other (OTH) AF: 0.00332 AC: 174 AN: 52456

GnomAD4 genome AF: 0.00309 AC: 462 AN: 149694 Hom.: 1 Cov.: 31 AF XY: 0.00300 AC XY: 219 AN XY: 73096

African (AFR) AF: 0.000679 AC: 28 AN: 41222

American (AMR) AF: 0.00238 AC: 36 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.0134 AC: 46 AN: 3428

East Asian (EAS) AF: 0.000197 AC: 1 AN: 5086

South Asian (SAS) AF: 0.00354 AC: 17 AN: 4798

European-Finnish (FIN) AF: 0.000922 AC: 9 AN: 9762

Middle Eastern (MID) AF: 0.00347 AC: 1 AN: 288

European-Non Finnish (NFE) AF: 0.00476 AC: 319 AN: 67022

Other (OTH) AF: 0.00240 AC: 5 AN: 2080

Alfa AF: 0.00442 Hom.: 0

Bravo AF: 0.00283

ClinVar

ClinVar submissions

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	15
DANN	Benign	0.96
PhyloP100		-0.045
Mutation Taster		=100/0	polymorphism

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: rs200769141; hg19: chr9-124461666;