5-52989814-G-GCACA

Variant summary

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

The NM_002203.4(ITGA2):c.64+301_64+304dup 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

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 5-52989814-G-GCACA is Benign according to our data. Variant chr5-52989814-G-GCACA is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA2	NM_002203.4	c.64+301_64+304dup		intron_variant		ENST00000296585.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA2	ENST00000296585.10	c.64+301_64+304dup		intron_variant		1	NM_002203.4	P1
ITGA2-AS1	ENST00000662246.1	n.75+275_75+276insTGTG		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.303

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs35389760; hg19: chr5-52285644;