rs756852335

Variant names:

• chr5-52989833-CACAG-C
• rs756852335
• NM_002203.4:c.64+309_64+312delGACA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002203.4(ITGA2):​c.64+309_64+312delGACA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 151,464 control chromosomes in the GnomAD database, including 2,623 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (2623 hom., cov: 24)
• Consequence: ITGA2 NM_002203.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.251
• Publications: 0 publications found

Genes affected

ITGA2 (HGNC:6137): (integrin subunit alpha 2) This gene encodes the alpha subunit of a transmembrane receptor for collagens and related proteins. The encoded protein forms a heterodimer with a beta subunit and mediates the adhesion of platelets and other cell types to the extracellular matrix. Loss of the encoded protein is associated with bleeding disorder platelet-type 9. Antibodies against this protein are found in several immune disorders, including neonatal alloimmune thrombocytopenia. This gene is located adjacent to a related alpha subunit gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

ITGA2-AS1 (HGNC:40306): (ITGA2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 5-52989833-CACAG-C is Benign according to our data. Variant chr5-52989833-CACAG-C is described in ClinVar as Benign. ClinVar VariationId is 1279129.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002203.4. 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
	ITGA2	NM_002203.4	MANE Select	c.64+309_64+312delGACA		intron	N/A	NP_002194.2	P17301
	ITGA2	NR_073103.2		n.181+309_181+312delGACA		intron	N/A
	ITGA2	NR_073104.2		n.181+309_181+312delGACA		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA2	ENST00000296585.10	TSL:1 MANE Select	c.64+302_64+305delACAG		intron	N/A	ENSP00000296585.5	P17301
	ITGA2	ENST00000509814.5	TSL:1	n.64+302_64+305delACAG		intron	N/A	ENSP00000424397.1	E7EMF1
	ITGA2	ENST00000509960.5	TSL:1	n.64+302_64+305delACAG		intron	N/A	ENSP00000424642.1	E9PB77

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26827 AN: 151354 Hom.: 2620 Cov.: 24

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.177 AC: 26825 AN: 151464 Hom.: 2623 Cov.: 24 AF XY: 0.176 AC XY: 13010 AN XY: 73942

African (AFR) AF: 0.108 AC: 4448 AN: 41374

American (AMR) AF: 0.168 AC: 2546 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1061 AN: 3460

East Asian (EAS) AF: 0.110 AC: 562 AN: 5100

South Asian (SAS) AF: 0.106 AC: 511 AN: 4800

European-Finnish (FIN) AF: 0.228 AC: 2379 AN: 10424

Middle Eastern (MID) AF: 0.250 AC: 72 AN: 288

European-Non Finnish (NFE) AF: 0.214 AC: 14547 AN: 67836

Other (OTH) AF: 0.200 AC: 420 AN: 2098

Alfa AF: 0.183 Hom.: 187

ClinVar

ClinVar submissions

Significance: 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
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs756852335; hg19: chr5-52285663;