rs3212478

chr5-53047731-A-Gchr5-53047731-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002203.4(ITGA2):c.388-632A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,080 control chromosomes in the GnomAD database, including 5,820 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (5820 hom., cov: 32)
• Consequence: ITGA2 NM_002203.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA2	NM_002203.4	c.388-632A>G		intron_variant		ENST00000296585.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA2	ENST00000296585.10	c.388-632A>G		intron_variant		1	NM_002203.4	P1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41747 AN: 151962 Hom.: 5819 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.275 AC: 41770 AN: 152080 Hom.: 5820 Cov.: 32 AF XY: 0.278 AC XY: 20654 AN XY: 74320

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.274

Alfa AF: 0.203 Hom.: 526

Bravo AF: 0.273

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.035
Dann	Benign	0.47

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: rs3212478; hg19: chr5-52343561;