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_000138.5(FBN1):c.59A>G (p.Tyr20Cys)

CA016208

161245 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: b564731f-1779-42d9-a066-ce2725ca6b48
Approved on: 2022-12-01
Published on: 2022-12-01

HGVS expressions

NM_000138.5:c.59A>G
NM_000138.5(FBN1):c.59A>G (p.Tyr20Cys)
NC_000015.10:g.48644711T>C
CM000677.2:g.48644711T>C
NC_000015.9:g.48936908T>C
CM000677.1:g.48936908T>C
NC_000015.8:g.46724200T>C
NG_008805.2:g.6078A>G
ENST00000316623.10:c.59A>G
ENST00000316623.9:c.59A>G
ENST00000537463.6:c.59A>G
ENST00000558230.1:n.122A>G
ENST00000560355.1:c.59A>G
NM_000138.4:c.59A>G
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Uncertain Significance

The Expert Panel has overridden the computationally generated classification - "Likely Benign"
Met criteria codes 2
BS1 BP2
Not Met criteria codes 23
BS4 BS3 BS2 BP7 BP5 BP3 BP4 BP1 PS2 PS3 PS1 BA1 PP4 PP1 PP3 PP2 PM6 PM2 PM4 PM3 PM1 PM5 PVS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen FBN1 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
The NM_000138 c.59A>G, is a missense variant in FBN1 predicted to cause a substitution of a Tyrosine by a Cysteine at amino acid 20 (p.Tyr20Cys). This variant was found in a proband with aortic root dilatation and a systemic score of 7 or above which is a highly specific phenotype for Marfan syndrome, however, a pathogenic splice variant in FBN1 was also identified in cis in this individual (BP2). The variant segregates with the disease in 4 affected family members, who also carry the pathogenic splice variant in FBN1. The variant in FBN1 has been reported 12 times in ClinVar: 3 times as likely benign, 8 times as uncertain significance and once as likely pathogenic (Variation ID: 161245). This variant has been identified in 37 individuals of European non-Finnish origin (MAF: 0.029%) (BS1; https://gnomad.broadinstitute.org/ version 2.1.1). The constraint z-score for missense variants affecting FBN1 is 5.06, however due to the presence of two benign arguments, PP2 cannot be used. In summary, this variant meets criteria to be classified as likely benign for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: BS1, BP2
Met criteria codes
BS1
Frequency in NF 0.029% which is between 0.005-0.1%
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
REVEL: 0.3659 which is just aboven the threshold of 0.326
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
The previously established pathogenic variant is causes a nonsense effect, which in opposition to a missense effect, it is mostly disease causing
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
Although patient has TAD and SS>7, mother known with EL, another pathogenic variant in FBN1 has been identified in this patient.
PP1
Segregates with 4 affected family members, however another FBN1 pathogenic variantin cis, has been found in all affected family members.
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
Other benign criteria have been applied. If this argument is used pro-pathogenicity, there must be other arguments supporting pathogenicity, and no arguments supporting a benign assertion
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
It's a Cys creating variant but in the signalling peptide, the effect here is not clear
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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