5-52989814-GCACACACACACA-GCACACACACACACACA

Variant names:

• chr5-52989814-G-GCACA
• rs35389760
• NM_002203.4:c.64+301_64+304dupCACA

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+301_64+304dupCACA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.32 (7184 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-GCACA is Benign according to our data. Variant chr5-52989814-G-GCACA is described in ClinVar as Benign. ClinVar VariationId is 1253474.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 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+301_64+304dupCACA		intron	N/A	NP_002194.2	P17301
	ITGA2	NR_073103.2		n.181+301_181+304dupCACA		intron	N/A
	ITGA2	NR_073104.2		n.181+301_181+304dupCACA		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+283insCACA		intron	N/A	ENSP00000296585.5	P17301
	ITGA2	ENST00000509814.5	TSL:1	n.64+282_64+283insCACA		intron	N/A	ENSP00000424397.1	E7EMF1
	ITGA2	ENST00000509960.5	TSL:1	n.64+282_64+283insCACA		intron	N/A	ENSP00000424642.1	E9PB77

Frequencies

GnomAD3 genomes AF: 0.316 AC: 45972 AN: 145550 Hom.: 7188 Cov.: 0

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.316 AC: 45988 AN: 145658 Hom.: 7184 Cov.: 0 AF XY: 0.316 AC XY: 22381 AN XY: 70822

African (AFR) AF: 0.257 AC: 10324 AN: 40174

American (AMR) AF: 0.314 AC: 4594 AN: 14616

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1054 AN: 3250

East Asian (EAS) AF: 0.124 AC: 615 AN: 4946

South Asian (SAS) AF: 0.337 AC: 1548 AN: 4598

European-Finnish (FIN) AF: 0.329 AC: 3163 AN: 9600

Middle Eastern (MID) AF: 0.330 AC: 89 AN: 270

European-Non Finnish (NFE) AF: 0.363 AC: 23708 AN: 65374

Other (OTH) AF: 0.303 AC: 602 AN: 1986

Alfa AF: 0.298 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;