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Variant: NM_001114753.3(ENG):c.1316A>C (p.Lys439Thr)

CA5252800

365088 (ClinVar)

Gene: ENG
Condition: telangiectasia, hereditary hemorrhagic, type 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 60a858c4-d5e2-4340-9711-47a9b5a5a012
Approved on: 2024-03-15
Published on: 2024-03-15

HGVS expressions

NM_001114753.3:c.1316A>C
NM_001114753.3(ENG):c.1316A>C (p.Lys439Thr)
NC_000009.12:g.127818828T>G
CM000671.2:g.127818828T>G
NC_000009.11:g.130581107T>G
CM000671.1:g.130581107T>G
NC_000009.10:g.129620928T>G
NG_009551.1:g.40941A>C
ENST00000480266.6:c.770A>C
ENST00000373203.9:c.1316A>C
ENST00000344849.4:c.1316A>C
ENST00000373203.8:c.1316A>C
ENST00000480266.5:c.770A>C
NM_000118.3:c.1316A>C
NM_001114753.2:c.1316A>C
NM_001278138.1:c.770A>C
NR_136302.1:n.1568+117T>G
NM_001278138.2:c.770A>C
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Likely Benign

Met criteria codes 3
BS1_Supporting BP4 BS3_Supporting

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 ENG Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Hemorrhagic Telangiectasia VCEP
The NM_001114753.3: c.1316A>C variant in ENG is a missense variant predicted to cause substitution of lysine by threonine at amino acid 439 (p.Lys439Thr). The filtering allele frequency (the lower threshold of the 95% CI of 15/10368) of the c.1316A>C variant in ENG is 0.0008918 for Ashkenazi Jewish chromosomes by gnomAD v2.1.1, which is higher than the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel threshold (>0.0008-0.002) for BS1_Supporting, and therefore meets this criterion (BS1_Supporting). The computational predictor REVEL gives a score of 0.041, which is below the threshold of ≤0.15, and the splice site predictor SpliceAI indicated that the variant has no impact on splicing, evidence that does not predict a damaging effect on ENG function (BP4). Additionally, functional assays showed the variant protein localized to the cell surface and had normal BMP9 response indicating that this variant does not impact protein function (BS3_Supporting; PMID: 25312062). 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_Supporting, BP4, BS3_Supporting (specification version 1.0.0; 1/4/2024).
Met criteria codes
BS1_Supporting
The filtering allele frequency (the lower threshold of the 95% CI of 15/10368) of the c.1316A>C variant in ENG is 0.0008918 for Ashkenazi Jewish chromosomes by gnomAD v2.1.1, which is higher than the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel threshold (>0.0008-0.002) for BS1_Supporting, and therefore meets this criterion (BS1_Supporting).
BP4
The computational predictor REVEL gives a score of 0.041, which is below the threshold of ≤0.15, and the splice site predictor SpliceAI indicated that the variant has no impact on splicing, evidence that does not predict a damaging effect on ENG function (BP4).
BS3_Supporting
Functional assays showed the variant protein localized to the cell surface and had normal BMP9 response indicating that this variant does not impact protein function (BS3_Supporting; PMID: 25312062).
Curation History
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