chr5-53094196-A-AATTTATAAACAACTTTGTAGGACT

Position:

• chr5-53094196-A-AATTTATAAACAACTTTGTAGGACT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_002203.4(ITGA2):​c.*3599_*3600insTTATAAACAACTTTGTAGGACTAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: 𝑓 0.10 (915 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ITGA2 NM_002203.4 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: 0.877

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGA2	NM_002203.4	c.*3599_*3600insTTATAAACAACTTTGTAGGACTAT		3_prime_UTR_variant	30/30	ENST00000296585.10	NP_002194.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA2	ENST00000296585.10	c.*3599_*3600insTTATAAACAACTTTGTAGGACTAT		3_prime_UTR_variant	30/30	1	NM_002203.4	ENSP00000296585.5

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15349 AN: 151910 Hom.: 912 Cov.: 0

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0604

Gnomad FIN AF: 0.0543

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.114

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 FIN exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.101 AC: 15386 AN: 152026 Hom.: 915 Cov.: 0 AF XY: 0.0969 AC XY: 7196 AN XY: 74292

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0808

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.0178

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.0543

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0344 Hom.: 341

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Platelet-type bleeding disorder 9 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

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: rs57674800; hg19: chr5-52390026;