rs27890

chr5-53030218-A-G

Variant summary

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

The NM_002203.4(ITGA2):c.185+3350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 152,326 control chromosomes in the GnomAD database, including 170 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 0.038 (170 hom., cov: 33)
• Consequence: ITGA2 NM_002203.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA2	NM_002203.4	c.185+3350A>G		intron_variant		ENST00000296585.10
LOC124900974	XR_007058767.1	n.132-3738T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA2	ENST00000296585.10	c.185+3350A>G		intron_variant		1	NM_002203.4	P1
	ENST00000652284.1	n.385+1532T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0382 AC: 5813 AN: 152208 Hom.: 170 Cov.: 33

Gnomad AFR AF: 0.0100

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0382 AC: 5814 AN: 152326 Hom.: 170 Cov.: 33 AF XY: 0.0375 AC XY: 2794 AN XY: 74474

Gnomad4 AFR AF: 0.0100

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.0651

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0363

Gnomad4 FIN AF: 0.0419

Gnomad4 NFE AF: 0.0574

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0507 Hom.: 115

Bravo AF: 0.0374

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.11
Dann	Benign	0.51

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: rs27890; hg19: chr5-52326048;