Genetic Variant ITGA2:c.185+287_185+290dupTAGA (chr5-53027152-T-TGATA) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002203.4(ITGA2):c.185+287_185+290dupTAGA 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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.168

Publications

0 publications found

Variant links:

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 Gene-Disease associations (from GenCC):

platelet-type bleeding disorder 9
Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ITGA2 links:

ENSG00000286048 (HGNC:):

ENSG00000286048 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002203.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ITGA2	NM_002203.4	MANE Select	c.185+287_185+290dupTAGA	intron	N/A	NP_002194.2	P17301
ITGA2	NR_073103.2		n.302+287_302+290dupTAGA	intron	N/A
ITGA2	NR_073104.2		n.302+287_302+290dupTAGA	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ITGA2	ENST00000296585.10	TSL:1 MANE Select	c.185+284_185+285insGATA	intron	N/A	ENSP00000296585.5	P17301
ITGA2	ENST00000509814.5	TSL:1	n.185+284_185+285insGATA	intron	N/A	ENSP00000424397.1	E7EMF1
ITGA2	ENST00000509960.5	TSL:1	n.185+284_185+285insGATA	intron	N/A	ENSP00000424642.1	E9PB77

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

28450

AN:

151932

Hom.:

2788

Cov.:

show subpopulations

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.:

AF XY:

0.189

AC XY:

14068

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.247

AC:

10254

AN:

41464

American (AMR)

AF:

0.129

AC:

1972

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0987

AC:

342

AN:

3466

East Asian (EAS)

AF:

0.0785

AC:

407

AN:

5184

South Asian (SAS)

AF:

0.157

AC:

757

AN:

4822

European-Finnish (FIN)

AF:

0.229

AC:

2427

AN:

10576

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.173

AC:

11776

AN:

67948

Other (OTH)

AF:

0.177

AC:

374

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1174

2348

3521

4695

5869

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

320

640

960

1280

1600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.197

Hom.:

279

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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5-53027152-TGATA-TGATAGATA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over