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Variant: NM_000020.3(ACVRL1):c.1445C>T (p.Ala482Val)

CA211324

161201 (ClinVar)

Gene: ACVRL1
Condition: telangiectasia, hereditary hemorrhagic, type 2
Inheritance Mode: Autosomal dominant inheritance
UUID: fdfbf530-02fb-4e07-b08b-a969443b1912
Approved on: 2024-03-15
Published on: 2024-03-15

HGVS expressions

NM_000020.3:c.1445C>T
NM_000020.3(ACVRL1):c.1445C>T (p.Ala482Val)
NC_000012.12:g.51920826C>T
CM000674.2:g.51920826C>T
NC_000012.11:g.52314610C>T
CM000674.1:g.52314610C>T
NC_000012.10:g.50600877C>T
NG_009549.1:g.18409C>T
ENST00000547400.6:c.1175C>T
ENST00000551576.6:c.1445C>T
ENST00000388922.9:c.1445C>T
ENST00000388922.8:c.1445C>T
ENST00000419526.6:c.923C>T
ENST00000550683.5:c.1487C>T
NM_000020.2:c.1445C>T
NM_001077401.1:c.1445C>T
NM_001077401.2:c.1445C>T
More

Likely Benign

Met criteria codes 5
PM5 BS3_Supporting BS1 BP5 PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hereditary Hemorrhagic Telangiectasia Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ACVRL1 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Hemorrhagic Telangiectasia VCEP
The NM_000020.3: c.1445C>T variant in ACVRL1 is a missense variant predicted to cause substitution of alanine by valine at amino acid 482 (p.Ala482Val). Another missense variant, c.1445C>A, Ala482Glu (PMID: 17786384, 21158752), in the same codon has been classified as likely pathogenic for autosomal dominant Hereditary Hemorrhagic Telangiectasia by the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel (PM5). However, the filtering allele frequency (the lower threshold of the 95% CI of 395/129122) of the c.1445C>T variant in ACVRL1 is 0.002819 for European (non-Finnish) chromosomes by gnomAD v2.1.1, which is higher than the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel threshold (>0.002) for BS1, and therefore meets this criterion (BS1). This variant has also been observed in 3 patients with an alternate molecular basis for disease (patients also carry a likely pathogenic/pathogenic ENG variant) (BP5; PMID: 15517393, Internal lab contributors). The computational predictor REVEL gives a score of 0.839, which is above the threshold of ≥0.644, evidence that correlates with impact to ACVRL1 function (PP3). However, functional assays (BRE assay, Western blot analysis of Smad1/5 phosphorylation) in NIH-3T3 cells showed that the variant protein responded to BMP9 stimulation either measured in the BRE assay or by Smad1/5 phosphorylation, indicating that this variant does not impact protein function (BS3_Supporting; PMID: 20501893). In summary, this variant meets the criteria to be classified as likely benign for autosomal dominant hereditary hemorrhagic telangiectasia based on the ACMG/AMP criteria applied, as specified by the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel: BS1, BP5, BS3_Supporting, PP3, PM5 (specification version 1.0.0; 1/4/2024).
Met criteria codes
PM5
Another missense variant, c.1445C>A, Ala482Glu (PMID: 17786384, 21158752), in the same codon has been classified as likely pathogenic for autosomal dominant Hereditary Hemorrhagic Telangiectasia by the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel (PM5).
BS3_Supporting
Functional assays (BRE assay, Western blot analysis of Smad1/5 phosphorylation) in NIH-3T3 cells showed that the variant protein responded to BMP9 stimulation either measured in the BRE assay or by Smad1/5 phosphorylation, indicating that this variant does not impact protein function (BS3_Supporting; PMID: 20501893).
BS1
The filtering allele frequency (the lower threshold of the 95% CI of 395/129122) of the c.1445C>T variant in ACVRL1 is 0.002819 for European (non-Finnish) chromosomes by gnomAD v2.1.1, which is higher than the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel threshold (>0.002) for BS1, and therefore meets this criterion (BS1).
BP5
This variant has been observed in 3 patients with an alternate molecular basis for disease (also carriers likely pathogenic/pathogenic ENG variant) (BP5; PMID: 15517393, Internal lab contributors).
PP3
The computational predictor REVEL gives a score of 0.839, which is above the threshold of ≥0.644, evidence that correlates with impact to ACVRL1 function (PP3).
Curation History
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