rs1062535
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_002203.4(ITGA2):c.825G>A(p.Thr275=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 1,612,484 control chromosomes in the GnomAD database, including 126,459 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.37 ( 10606 hom., cov: 32)
Exomes 𝑓: 0.40 ( 115853 hom. )
Consequence
ITGA2
NM_002203.4 synonymous
NM_002203.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.427
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 -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant 5-53055583-G-A is Benign according to our data. Variant chr5-53055583-G-A is described in ClinVar as [Benign]. Clinvar id is 353744.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-53055583-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.427 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA2 | NM_002203.4 | c.825G>A | p.Thr275= | synonymous_variant | 8/30 | ENST00000296585.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA2 | ENST00000296585.10 | c.825G>A | p.Thr275= | synonymous_variant | 8/30 | 1 | NM_002203.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.372 AC: 56486AN: 151744Hom.: 10601 Cov.: 32
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GnomAD3 exomes AF: 0.388 AC: 97173AN: 250348Hom.: 19154 AF XY: 0.387 AC XY: 52334AN XY: 135246
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GnomAD4 exome AF: 0.396 AC: 578730AN: 1460620Hom.: 115853 Cov.: 38 AF XY: 0.395 AC XY: 287134AN XY: 726640
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GnomAD4 genome ? AF: 0.372 AC: 56517AN: 151864Hom.: 10606 Cov.: 32 AF XY: 0.372 AC XY: 27626AN XY: 74184
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Platelet-type bleeding disorder 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | This variant is associated with the following publications: (PMID: 9950439) - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at