Variant: NM_000419.5(ITGA2B):c.2348+15G>A

Version: 2.0
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CA8602722

890528 (ClinVar)

Gene: ITGA2B (HGNC:3674)

Condition: Glanzmann thrombasthenia

Inheritance Mode: Autosomal recessive inheritance

UUID: 01b0c1b1-ac6f-4eaa-ac15-14754a14eba4

Approved on: 2025-02-18

Published on: 2025-02-18

HGVS expressions

NM_000419.5:c.2348+15G>A
NM_000419.5(ITGA2B):c.2348+15G>A
NC_000017.11:g.44376293C>T
CM000679.2:g.44376293C>T
NC_000017.10:g.42453661C>T
CM000679.1:g.42453661C>T
NC_000017.9:g.39809187C>T
NG_008331.1:g.18213G>A
ENST00000262407.6:c.2348+15G>A
ENST00000648408.1:c.1779+15G>A
ENST00000262407.5:c.2348+15G>A
ENST00000592462.5:n.1143+15G>A
NM_000419.3:c.2348+15G>A
NM_000419.4:c.2348+15G>A

Likely Benign

• Met criteria codes: BP7 BP4

• Not Met criteria codes: PM2 BS1

Expert Panel

Platelet Disorders VCEP

Criteria Specification Information

Criteria Specification: ClinGen Platelet Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2.1

Evidence submitted by expert panel

Platelet Disorders VCEP

The NM_000419.5(ITGA2B):c.2348+15G>A variant is an intronic variant that is not predicted by SpliceAI to impact splicing (Delta scores <0.03). In addition, it occurs at a nucleotide that is not conserved as shown by phyloP score of -1.96 (BP7). The highest population minor allele frequency in gnomAD v4.0.0 is 0.0003737 (441/1179990 alleles) in the European (non-Finnish) population. This intermediate allele frequency is lower than the ClinGen PD VCEP threshold (>0.00158) for BS1 but higher than the threshold (<0.0001) for PM2_Supporting. In summary this variant is classified as likely benign for autosomal recessive Glanzmann thrombasthenia, with ACMG criteria applied as specified by the PD VCEP: BP4, BP7

Met criteria codes

• BP7: The NM_000419.5(ITGA2B):c.2348+15G>A variant is an intronic variant that is not predicted by SpliceAI to impact splicing (Delta scores <0.03). In addition, it occurs at a nucleotide that is not conserved as shown by phyloP score of -1.96 (BP7).
• BP4: an intronic variant that is not predicted by SpliceAI to impact splicing (Delta scores <0.03)

Not Met criteria codes

• PM2: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BS1: The highest population minor allele frequency in gnomAD v4.0.0 is 0.0003737 (441/1179990 alleles) in the European (non-Finnish) population. This intermediate allele frequency is lower than the ClinGen PD VCEP threshold (>0.00158) for BS1 but higher than the threshold (<0.0001) for PM2_Supporting.