The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000020.3(ACVRL1):c.1232G>A (p.Arg411Gln)

CA119395

8243 (ClinVar)

Gene: ACVRL1
Condition: telangiectasia, hereditary hemorrhagic, type 2
Inheritance Mode: Autosomal dominant inheritance
UUID: ed2b5ccd-ee24-43e2-bed3-c10a3a4e0706

HGVS expressions

NM_000020.3:c.1232G>A
NM_000020.3(ACVRL1):c.1232G>A (p.Arg411Gln)
NC_000012.12:g.51916219G>A
CM000674.2:g.51916219G>A
NC_000012.11:g.52310003G>A
CM000674.1:g.52310003G>A
NC_000012.10:g.50596270G>A
NG_009549.1:g.13802G>A
ENST00000547400.6:c.962G>A
ENST00000551576.6:c.1232G>A
ENST00000552678.2:c.1232G>A
ENST00000388922.9:c.1232G>A
ENST00000388922.8:c.1232G>A
ENST00000419526.6:c.710G>A
ENST00000547632.1:n.507G>A
ENST00000550683.5:c.1274G>A
ENST00000552678.1:c.237G>A
NM_000020.2:c.1232G>A
NM_001077401.1:c.1232G>A
NM_001077401.2:c.1232G>A

Pathogenic

Met criteria codes 6
PM2_Supporting PS3_Supporting PP4_Moderate PS4 PP3 PP1_Strong

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.1232G>A variant in ACVRL1 is a missense variant predicted to cause substitution of arginine by glutamine at amino acid 411 (p.Arg411Gln). The overall minor allele frequency in gnomAD v2.1.1 is 0.000007980 (2/250642 alleles), which is lower than the ClinGen Hereditary Hemorrhagic Telangiectasia VCEP threshold (<6 total alleles) for PM2_Supporting, meeting this criterion (PM2_Supporting). This variant has been reported in >10 probands with a phenotype consistent with HHT (PS4; PMID: 8640225, 31400083, 32300199, Internal lab contributors). At least one patient's phenotype meets Curacao Criteria for HHT, and sequencing and large deletion/duplication analysis was performed for ENG and ACVRL1, which is highly specific for HHT (PP4_Moderate; PMID: 32300199). The variant has been reported to segregate with HHT in 8 affected family members from one family (PP1_Strong; PMID: 8640225). The computational predictor REVEL gives a score of 0.904, which is above the threshold of ≥0.644, evidence that correlates with impact to ACVRL1 function (PP3). Additionally, binding assays in cell lines showed no BMP9 response indicating that this variant impacts protein function (PS3_Supporting; PMID: 20501893). In summary, this variant meets the criteria to be classified as pathogenic 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: PS4, PP1_Strong, PP4_Moderate, PM2_Supporting, PP3, PS3_Supporting (specification version 1.0.0; 1/4/2024).
Met criteria codes
PM2_Supporting
The overall minor allele frequency in gnomAD v2.1.1 is 0.000007980 (2/250642 alleles), which is lower than the ClinGen Hereditary Hemorrhagic Telangiectasia VCEP threshold (<6 total alleles) for PM2_Supporting, meeting this criterion (PM2_Supporting).
PS3_Supporting
Binding assays in cell lines showed no BMP9 response indicating that this variant impacts protein function (PS3_Supporting; PMID: 20501893).
PP4_Moderate
At least one patient's phenotype meets Curacao Criteria for HHT, and sequencing and large deletion/duplication analysis was performed for ENG and ACVRL1, which is highly specific for HHT (PP4_Moderate; PMID: 32300199).
PS4
This variant has been reported in >10 probands with a phenotype consistent with HHT (PS4; PMID: 8640225, 31400083, 32300199, Internal lab contributors).
PP3
The computational predictor REVEL gives a score of 0.904, which is above the threshold of ≥0.644, evidence that correlates with impact to ACVRL1 function (PP3).
PP1_Strong
The variant has been reported to segregate with HHT in 8 affected family members from one family (PP1_Strong; PMID: 8640225).
Approved on: 2024-03-15
Published on: 2024-03-15
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.