5-52989833-CACAG-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002203.4(ITGA2):c.64+309_64+312del 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

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

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA2	NM_002203.4	c.64+309_64+312del		intron_variant		ENST00000296585.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA2	ENST00000296585.10	c.64+309_64+312del		intron_variant		1	NM_002203.4	P1
ITGA2-AS1	ENST00000662246.1	n.75+253_75+256del		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.200

Alfa AF: 0.183 Hom.: 187

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs756852335; hg19: chr5-52285663;