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.88C>T (p.Pro30Ser)

CA211326

161202 (ClinVar)

Gene: ACVRL1
Condition: telangiectasia, hereditary hemorrhagic, type 2
Inheritance Mode: Autosomal dominant inheritance
UUID: d20c8a14-bab7-42df-9add-f5ff912fa0d5

HGVS expressions

NM_000020.3:c.88C>T
NM_000020.3(ACVRL1):c.88C>T (p.Pro30Ser)
NC_000012.12:g.51913125C>T
CM000674.2:g.51913125C>T
NC_000012.11:g.52306909C>T
CM000674.1:g.52306909C>T
NC_000012.10:g.50593176C>T
NG_009549.1:g.10708C>T
ENST00000547400.6:c.130C>T
ENST00000551576.6:c.88C>T
ENST00000552678.2:c.88C>T
ENST00000388922.9:c.88C>T
ENST00000388922.8:c.88C>T
ENST00000419526.6:c.103+590C>T
ENST00000547400.5:c.130C>T
ENST00000550683.5:c.130C>T
ENST00000551576.5:c.88C>T
NM_000020.2:c.88C>T
NM_001077401.1:c.88C>T
NM_001077401.2:c.88C>T

Likely Benign

Met criteria codes 2
BP2 BP5
Not Met criteria codes 2
PP3 PM2

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.88C>T variant in ACVRL1 is a missense variant predicted to cause substitution of proline by serine at amino acid 30 (p.Pro30Ser). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0004916 (17/34584 alleles) in the Admixed American population. This variant has been observed in 1 patient with an alternate molecular basis for disease (patient also carries a likely pathogenic/pathogenic ENG variant) (BP5; PMID: 32573726). This variant has been observed in trans with the variant c.191delA, p.Gln64Argfs*58 (PMID: 16752392), which is classified as pathogenic by the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel, in an individual with Hereditary Hemorrhagic Telangiectasia. The phase of the variants was confirmed by family testing (BP2). The computational predictor REVEL gives a score of 0.499, which is neither above nor below the thresholds predicting a damaging or benign impact on ACVRL1 function. 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: BP2, BP5 (specification version 1.0.0; 1/4/2024).
Met criteria codes
BP2
This variant has been observed in trans with the variant c.191delA, p.Gln64Argfs*58 (PMID: 16752392), which is classified as pathogenic by the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel, in an individual with Hereditary Hemorrhagic Telangiectasia. The phase of the variants was confirmed by family testing (BP2).
BP5
This variant has been observed in 1 patient with an alternate molecular basis for disease (patient also carries a likely pathogenic/pathogenic ENG variant) (BP5; PMID: 32573726).
Not Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.499, which is neither above nor below the thresholds predicting a damaging or benign impact on ACVRL1 function.
PM2
The highest population minor allele frequency in gnomAD v2.1.1 is 0.0004916 (17/34584 alleles) in the Admixed American population.
Approved on: 2024-03-15
Published on: 2024-03-15
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