rs6880055

Positions:

• chr5-53093598-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000296585.10(ITGA2):​c.*2999A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,062 control chromosomes in the GnomAD database, including 7,512 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.31 (7512 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ITGA2 ENST00000296585.10 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.0820

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP6: Variant 5-53093598-A-G is Benign according to our data. Variant chr5-53093598-A-G is described in ClinVar as [Benign]. Clinvar id is 353840.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGA2	NM_002203.4	c.*2999A>G		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.*2999A>G		3_prime_UTR_variant	30/30	1	NM_002203.4	ENSP00000296585	P1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47212 AN: 151944 Hom.: 7510 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.311 AC: 47227 AN: 152062 Hom.: 7512 Cov.: 32 AF XY: 0.313 AC XY: 23275 AN XY: 74326

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.313

Alfa AF: 0.337 Hom.: 1076

Bravo AF: 0.306

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Platelet-type bleeding disorder 9 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Combined molybdoflavoprotein enzyme deficiency Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.3
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs6880055; hg19: chr5-52389428;