5-52989814-GCACACACACACA-GCACACACACACACACACACA

Variant names:

• chr5-52989814-G-GCACACACA
• rs35389760
• NM_002203.4:c.64+297_64+304dupCACACACA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_002203.4(ITGA2):​c.64+297_64+304dupCACACACA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.020 (59 hom., cov: 0)
• Consequence: ITGA2 NM_002203.4 intron
• Clinical Significance: Not reported in ClinVar
• 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0899 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+297_64+304dupCACACACA		intron	N/A	NP_002194.2	P17301
	ITGA2	NR_073103.2		n.181+297_181+304dupCACACACA		intron	N/A
	ITGA2	NR_073104.2		n.181+297_181+304dupCACACACA		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+283insCACACACA		intron	N/A	ENSP00000296585.5	P17301
	ITGA2	ENST00000509814.5	TSL:1	n.64+282_64+283insCACACACA		intron	N/A	ENSP00000424397.1	E7EMF1
	ITGA2	ENST00000509960.5	TSL:1	n.64+282_64+283insCACACACA		intron	N/A	ENSP00000424642.1	E9PB77

Frequencies

GnomAD3 genomes AF: 0.0204 AC: 2979 AN: 145808 Hom.: 59 Cov.: 0

Gnomad AFR AF: 0.00817

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0121

Gnomad ASJ AF: 0.00799

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.0196

Gnomad MID AF: 0.0207

Gnomad NFE AF: 0.0209

Gnomad OTH AF: 0.0193

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

GnomAD4 genome AF: 0.0204 AC: 2981 AN: 145918 Hom.: 59 Cov.: 0 AF XY: 0.0217 AC XY: 1540 AN XY: 70954

African (AFR) AF: 0.00817 AC: 329 AN: 40272

American (AMR) AF: 0.0122 AC: 179 AN: 14640

Ashkenazi Jewish (ASJ) AF: 0.00799 AC: 26 AN: 3256

East Asian (EAS) AF: 0.0806 AC: 399 AN: 4950

South Asian (SAS) AF: 0.0974 AC: 448 AN: 4600

European-Finnish (FIN) AF: 0.0196 AC: 189 AN: 9638

Middle Eastern (MID) AF: 0.0222 AC: 6 AN: 270

European-Non Finnish (NFE) AF: 0.0209 AC: 1366 AN: 65454

Other (OTH) AF: 0.0196 AC: 39 AN: 1992

Alfa AF: 0.0225 Hom.: 338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.060
Mutation Taster		=100/0	polymorphism

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;