5-52989837-G-C

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.64+305G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 139,256 control chromosomes in the GnomAD database, including 36,140 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.74 (36140 hom., cov: 24)
• Consequence: ITGA2 NM_002203.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.60

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]

ITGA2-AS1 (HGNC:40306): (ITGA2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 5-52989837-G-C is Benign according to our data. Variant chr5-52989837-G-C is described in ClinVar as [Benign]. Clinvar id is 1281037.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGA2	NM_002203.4	c.64+305G>C		intron_variant		ENST00000296585.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGA2	ENST00000296585.10	c.64+305G>C		intron_variant		1	NM_002203.4	P1
ITGA2-AS1	ENST00000662246.1	n.75+253C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.744 AC: 103553 AN: 139154 Hom.: 36107 Cov.: 24

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.744 AC: 103640 AN: 139256 Hom.: 36140 Cov.: 24 AF XY: 0.746 AC XY: 50681 AN XY: 67928

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.749

Alfa AF: 0.706 Hom.: 2890

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

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.9
Dann	Benign	0.24

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: rs40118; hg19: chr5-52285667;