5-53026539-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_002203.4(ITGA2):c.65-209G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 152,192 control chromosomes in the GnomAD database, including 332 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.055 (332 hom., cov: 33)
• Consequence: ITGA2 NM_002203.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0460

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 5-53026539-G-A is Benign according to our data. Variant chr5-53026539-G-A is described in ClinVar as [Benign]. Clinvar id is 1180869.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.081 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA2	NM_002203.4	c.65-209G>A		intron_variant		ENST00000296585.10
LOC124900974	XR_007058767.1	n.132-59C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA2	ENST00000296585.10	c.65-209G>A		intron_variant		1	NM_002203.4	P1
	ENST00000652284.1	n.386-59C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8437 AN: 152074 Hom.: 332 Cov.: 33

Gnomad AFR AF: 0.0135

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0398

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0828

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0554 AC: 8433 AN: 152192 Hom.: 332 Cov.: 33 AF XY: 0.0559 AC XY: 4156 AN XY: 74392

Gnomad4 AFR AF: 0.0134

Gnomad4 AMR AF: 0.0397

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0305

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0828

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0669 Hom.: 49

Bravo AF: 0.0485

Asia WGS AF: 0.0160 AC: 55 AN: 3478

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 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.8
Dann	Benign	0.65

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: rs3212666; hg19: chr5-52322369;