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_000138.4(FBN1):c.8363C>T (p.Thr2788Met)

CA059963

263832 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: a1d82f83-e29b-4022-a4ae-7d95a9d27888
Approved on: 2023-02-01
Published on: 2023-02-01

HGVS expressions

NM_000138.4:c.8363C>T
NM_000138.4(FBN1):c.8363C>T (p.Thr2788Met)
NC_000015.10:g.48411243G>A
CM000677.2:g.48411243G>A
NC_000015.9:g.48703440G>A
CM000677.1:g.48703440G>A
NC_000015.8:g.46490732G>A
NG_008805.2:g.239546C>T
ENST00000682158.1:n.1744C>T
ENST00000682170.1:n.2544C>T
ENST00000682767.1:n.1660C>T
ENST00000316623.10:c.8363C>T
ENST00000674301.1:n.3529C>T
ENST00000316623.9:c.8363C>T
ENST00000559133.5:n.3732C>T
ENST00000561429.1:n.618C>T
NM_000138.5:c.8363C>T
NM_000138.5(FBN1):c.8363C>T (p.Thr2788Met)

Benign

Met criteria codes 1
BA1
Not Met criteria codes 25
PS2 PS4 PS3 PS1 PP4 PP1 PP3 PP2 PM6 PM2 PM3 PM1 PM4 PM5 BS2 BS4 BS3 BS1 BP5 BP7 BP2 BP3 BP4 BP1 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_00138 c.8363C>T, is a missense variant in FBN1 predicted to cause a substitution of a threonine by methionine at amino acid 2788 (p.Thr2788Met). The variant in FBN1 has been reported 13 times in ClinVar: 12 times as likely benign and once as benign (Variation ID: 263832). This variant has been identified in 44 individuals of African origin (gnomAD version 3.1.1, MAF: 0.1%, one homozygous) (BA1; https://gnomad.broadinstitute.org/). Computational prediction tools and conservation analysis are unclear on the predicted impact on the protein (REVEL: 0.356). The constraint z-score for missense variants affecting FBN1 is 5.06, however due to the presence of benign arguments PP2 cannot be used. In summary, this variant meets criteria to be classified as benign for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: BA1.
Met criteria codes
BA1
gnomAD v3.1,1 African/ African American frequency: 0.1% (44/41400) gnomAD v2.1.1: African/ African American frequency: 0.096% (24/24968)
Not Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Variant meets BS1, therefore although found in several probands with suspicion of MFS or TAD, this criterium cannot be used
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL score: 0.356
PP2
Due to the presence of benign arguments, PP2 cannot be applied.
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
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
Missense variant
PM5
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
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
BS1
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
BP7
Missense variant
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
Missense variant
BP4
REVEL score: 0.356
BP1
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
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