NM_001395010.1:c.363-19312G>A

Variant names:

• chr9-121737701-G-A
• rs145251128
• NM_001395010.1:c.363-19312G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001395010.1(DAB2IP):​c.363-19312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 985,438 control chromosomes in the GnomAD database, including 13 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: 33)
  • Exomes 𝑓: 0.0034 (12 hom.)
• Consequence: DAB2IP NM_001395010.1 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.83
• Publications: 0 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=-0.83).
• BP6: Variant 9-121737701-G-A is Benign according to our data. Variant chr9-121737701-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2659479.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 479 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.363-19312G>A		intron	N/A	NP_001381939.1	Q5VWQ8-1
	DAB2IP	NM_032552.4		c.279-19312G>A		intron	N/A	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.363-19312G>A		intron	N/A	ENSP00000386183.3	Q5VWQ8-1
	DAB2IP	ENST00000648444.1		c.165G>A	p.Ala55Ala	synonymous	Exon 1 of 14	ENSP00000497706.1	A0A3B3ITG3
	DAB2IP	ENST00000259371.7	TSL:5	c.279-19312G>A		intron	N/A	ENSP00000259371.2	Q5VWQ8-5

Frequencies

GnomAD3 genomes AF: 0.00315 AC: 479 AN: 152210 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000627

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00249

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00494

Gnomad OTH AF: 0.00239

GnomAD4 exome AF: 0.00338 AC: 2820 AN: 833110 Hom.: 12 Cov.: 29 AF XY: 0.00343 AC XY: 1321 AN XY: 384714

African (AFR) AF: 0.000253 AC: 4 AN: 15786

American (AMR) AF: 0.00 AC: 0 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.0151 AC: 78 AN: 5152

East Asian (EAS) AF: 0.00 AC: 0 AN: 3630

South Asian (SAS) AF: 0.00389 AC: 64 AN: 16460

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 276

Middle Eastern (MID) AF: 0.000617 AC: 1 AN: 1620

European-Non Finnish (NFE) AF: 0.00340 AC: 2589 AN: 761904

Other (OTH) AF: 0.00308 AC: 84 AN: 27298

GnomAD4 genome AF: 0.00314 AC: 479 AN: 152328 Hom.: 1 Cov.: 33 AF XY: 0.00305 AC XY: 227 AN XY: 74486

African (AFR) AF: 0.000625 AC: 26 AN: 41576

American (AMR) AF: 0.00248 AC: 38 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.00269 AC: 13 AN: 4828

European-Finnish (FIN) AF: 0.00113 AC: 12 AN: 10618

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00494 AC: 336 AN: 68036

Other (OTH) AF: 0.00237 AC: 5 AN: 2114

Alfa AF: 0.00138 Hom.: 0

Bravo AF: 0.00297

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.71
DANN	Benign	0.82
PhyloP100		-1.8
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: rs145251128; hg19: chr9-124499980;