5-52989814-GCACACACACACA-GCACACACACACACA

Variant names:

• chr5-52989814-G-GCA
• rs35389760
• NM_002203.4:c.64+303_64+304dupCA

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+303_64+304dupCA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.26 (4743 hom., cov: 0)
• Consequence: ITGA2 NM_002203.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0600
• Publications: 1 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 5-52989814-G-GCA is Benign according to our data. Variant chr5-52989814-G-GCA is described in ClinVar as Benign. ClinVar VariationId is 1261291.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 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+303_64+304dupCA		intron	N/A	NP_002194.2	P17301
	ITGA2	NR_073103.2		n.181+303_181+304dupCA		intron	N/A
	ITGA2	NR_073104.2		n.181+303_181+304dupCA		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+282_64+283insCA		intron	N/A	ENSP00000296585.5	P17301
	ITGA2	ENST00000509814.5	TSL:1	n.64+282_64+283insCA		intron	N/A	ENSP00000424397.1	E7EMF1
	ITGA2	ENST00000509960.5	TSL:1	n.64+282_64+283insCA		intron	N/A	ENSP00000424642.1	E9PB77

Frequencies

GnomAD3 genomes AF: 0.258 AC: 37544 AN: 145454 Hom.: 4738 Cov.: 0

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.262

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.258 AC: 37564 AN: 145558 Hom.: 4743 Cov.: 0 AF XY: 0.258 AC XY: 18244 AN XY: 70774

African (AFR) AF: 0.242 AC: 9713 AN: 40188

American (AMR) AF: 0.342 AC: 4991 AN: 14602

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 630 AN: 3252

East Asian (EAS) AF: 0.362 AC: 1788 AN: 4946

South Asian (SAS) AF: 0.234 AC: 1073 AN: 4594

European-Finnish (FIN) AF: 0.240 AC: 2288 AN: 9538

Middle Eastern (MID) AF: 0.270 AC: 73 AN: 270

European-Non Finnish (NFE) AF: 0.249 AC: 16301 AN: 65336

Other (OTH) AF: 0.265 AC: 527 AN: 1986

Alfa AF: 0.184 Hom.: 338

ClinVar

ClinVar submissions as Germline

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		-0.060
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs35389760; hg19: chr5-52285644;