5-53066935-A-T

Position:

• chr5-53066935-A-T

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.1944-183A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 150,428 control chromosomes in the GnomAD database, including 3,301 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.20 (3301 hom., cov: 32)
• Consequence: ITGA2 NM_002203.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.522

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 5-53066935-A-T is Benign according to our data. Variant chr5-53066935-A-T is described in ClinVar as [Benign]. Clinvar id is 1277623.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGA2	NM_002203.4	c.1944-183A>T		intron_variant		ENST00000296585.10	NP_002194.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA2	ENST00000296585.10	c.1944-183A>T		intron_variant		1	NM_002203.4	ENSP00000296585.5

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29408 AN: 150316 Hom.: 3294 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.196 AC: 29432 AN: 150428 Hom.: 3301 Cov.: 32 AF XY: 0.200 AC XY: 14664 AN XY: 73384

Gnomad4 AFR AF: 0.0691

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.200

Alfa AF: 0.205 Hom.: 483

Bravo AF: 0.181

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 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.088

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: rs3212556; hg19: chr5-52362765; COSMIC: COSV56857265;