dbSNP rs40118: ITGA2:c.64+305G>C (chr5-52989837-G-C) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.60

Publications

1 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 links:

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

ITGA2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

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.64+305G>C	intron	N/A	NP_002194.2	P17301
ITGA2	NR_073103.2		n.181+305G>C	intron	N/A
ITGA2	NR_073104.2		n.181+305G>C	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ITGA2	ENST00000296585.10	TSL:1 MANE Select	c.64+305G>C	intron	N/A	ENSP00000296585.5	P17301
ITGA2	ENST00000509814.5	TSL:1	n.64+305G>C	intron	N/A	ENSP00000424397.1	E7EMF1
ITGA2	ENST00000509960.5	TSL:1	n.64+305G>C	intron	N/A	ENSP00000424642.1	E9PB77

Frequencies

GnomAD3 genomes

AF:

0.744

AC:

103553

AN:

139154

Hom.:

36107

Cov.:

show subpopulations

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.:

AF XY:

0.746

AC XY:

50681

AN XY:

67928

show subpopulations

African (AFR)

AF:

0.653

AC:

24597

AN:

37686

American (AMR)

AF:

0.788

AC:

11112

AN:

14100

Ashkenazi Jewish (ASJ)

AF:

0.744

AC:

2279

AN:

3062

East Asian (EAS)

AF:

0.650

AC:

3017

AN:

4640

South Asian (SAS)

AF:

0.836

AC:

3809

AN:

4556

European-Finnish (FIN)

AF:

0.772

AC:

7237

AN:

9376

Middle Eastern (MID)

AF:

0.732

AC:

183

AN:

250

European-Non Finnish (NFE)

AF:

0.786

AC:

49500

AN:

62966

Other (OTH)

AF:

0.749

AC:

1411

AN:

1884

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

1338

2676

4015

5353

6691

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

814

1628

2442

3256

4070

<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:

0.706

Hom.:

2890

ClinVar

ClinVar submissions

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

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.9

(source)

DANN

Benign

0.24

PhyloP100

-1.6

PromoterAI

0.016

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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