rs3797497

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002203.4(ITGA2):​c.186-3624G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,926 control chromosomes in the GnomAD database, including 10,701 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.37 ( 10701 hom., cov: 31)

Consequence

ITGA2
NM_002203.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.427
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ITGA2NM_002203.4 linkuse as main transcriptc.186-3624G>A intron_variant ENST00000296585.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ITGA2ENST00000296585.10 linkuse as main transcriptc.186-3624G>A intron_variant 1 NM_002203.4 P1

Frequencies

GnomAD3 genomes
AF:
0.369
AC:
56084
AN:
151808
Hom.:
10684
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.308
Gnomad AMI
AF:
0.329
Gnomad AMR
AF:
0.356
Gnomad ASJ
AF:
0.456
Gnomad EAS
AF:
0.213
Gnomad SAS
AF:
0.396
Gnomad FIN
AF:
0.382
Gnomad MID
AF:
0.452
Gnomad NFE
AF:
0.413
Gnomad OTH
AF:
0.395
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.370
AC:
56156
AN:
151926
Hom.:
10701
Cov.:
31
AF XY:
0.367
AC XY:
27213
AN XY:
74220
show subpopulations
Gnomad4 AFR
AF:
0.309
Gnomad4 AMR
AF:
0.357
Gnomad4 ASJ
AF:
0.456
Gnomad4 EAS
AF:
0.214
Gnomad4 SAS
AF:
0.396
Gnomad4 FIN
AF:
0.382
Gnomad4 NFE
AF:
0.413
Gnomad4 OTH
AF:
0.394
Alfa
AF:
0.326
Hom.:
1829
Bravo
AF:
0.361
Asia WGS
AF:
0.303
AC:
1056
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
2.5
DANN
Benign
0.62

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3797497; hg19: chr5-52334318; COSMIC: COSV56857821; API