5-53027152-T-TGATA

Position:

• chr5-53027152-T-TGATA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002203.4(ITGA2):​c.185+287_185+290dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,050 control chromosomes in the GnomAD database, including 2,801 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (2801 hom., cov: 28)
• Consequence: ITGA2 NM_002203.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.168

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 -10 ACMG points.

• BP6: Variant 5-53027152-T-TGATA is Benign according to our data. Variant chr5-53027152-T-TGATA is described in ClinVar as [Benign]. Clinvar id is 1275434.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGA2	NM_002203.4	c.185+287_185+290dup		intron_variant		ENST00000296585.10	NP_002194.2
LOC124900974	XR_007058767.1	n.132-673_132-672insTATC		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA2	ENST00000296585.10	c.185+287_185+290dup		intron_variant		1	NM_002203.4	ENSP00000296585	P1
	ENST00000652284.1	n.386-673_386-672insTATC		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28450 AN: 151932 Hom.: 2788 Cov.: 28

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0987

Gnomad EAS AF: 0.0783

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.187 AC: 28499 AN: 152050 Hom.: 2801 Cov.: 28 AF XY: 0.189 AC XY: 14068 AN XY: 74334

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0987

Gnomad4 EAS AF: 0.0785

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.177

Alfa AF: 0.197 Hom.: 279

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

Nov 12, 2018

- -

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: rs3212422; hg19: chr5-52322982;