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Variant: NM_000138.5(FBN1):c.4640C>T (p.Thr1547Ile)

CA015264

42367 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: d2dbabeb-c2f7-48bd-bc81-757034edd0e6

HGVS expressions

NM_000138.5:c.4640C>T
NM_000138.5(FBN1):c.4640C>T (p.Thr1547Ile)
NC_000015.10:g.48468045G>A
CM000677.2:g.48468045G>A
NC_000015.9:g.48760242G>A
CM000677.1:g.48760242G>A
NC_000015.8:g.46547534G>A
NG_008805.2:g.182744C>T
ENST00000684448.1:n.3314C>T
ENST00000316623.10:c.4640C>T
ENST00000316623.9:c.4640C>T
ENST00000537463.6:c.*403C>T
NM_000138.4:c.4640C>T

Benign

Met criteria codes 1
BA1
Not Met criteria codes 16
PS3 PS2 PS4 PP1 PP4 PP3 PP2 PM1 PM6 PM2 BS3 BS4 BS1 BP5 BP2 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
The NM_00138 c.4640C>T, is a missense variant in FBN1 predicted to cause a substitution of a threonine by isoleucine at amino acid 1547 (p.Thr1547Ile). This variant was found one proband with Marfan syndrome (PMID 24793577) and in three apparently unrelated probands with features of Marfan syndrome (PMID 24793577, internal data). In one of these individuals with features of Marfan syndrome, this variant was also detected in the proband’s mother and sister, both of whom had a systemic score of 9, however relatedness of these individuals was not confirmed (internal data). This variant was also identified in an individual with features of Marfan syndrome but no diagnosis who also carried a pathogenic variant in FBN1, c.3193delG p.Glu1065Lysfs*23 (PMID 29543232). The variant in FBN1 has been reported 17 times in ClinVar: 6 times as uncertain significance and 11 times as likely benign (Variation ID: 42367). This variant has been identified in 37 individuals of Latino/Admixed American origin in gnomAD v3.1.2 (MAF: 0.24%) (BA1; https://gnomad.broadinstitute.org/). Computational prediction tools and conservation analysis are unclear on the predicted impact on the protein (REVEL: 0.375). 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: 0.2% (37/15268) of Latino/Admixed American alleles
Not Met criteria codes
PS3
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
PS4
Although this variant has been found in 3 probands with Marfan or Marfan-like phenotype, PS4 should not apply due to high prevalence in the general population
PP1
PP1: N<=1/2 in a single family: Proband, mother and sibling all have this variant and skeletal features. Sibling also has MVP.
PP4
Definition highly specific phenotype: TAAD + ectopia lentis Proband, mother and sibling all have this variant and skeletal features. Sibling also has Mitral Valve Prolapse. Proband's phenotype wasn't provided beyond "diagnosis of MFS"
PP3
In silico tools are conflicting. REVEL score: 0.375 CADD score: 1.98 MetaLR score: 0.51
PP2
Based on the SVI WG recommendation concerning constraint scores: if missense constraint z scores are > 3.09 in ExAC, this criterion may be used. For FBN1, the constraint score is higher than 5. Hence, PP2 is applicable as described. However, the EP wishes to include a caveat (if this argument is used pro-pathogenicity, there must be other arguments supporting pathogenicity, and no arguments supporting a benign assertion).
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
BS3
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
BS1
Variant found in 5/35440 (0.014%) in Latino alleles in gnomAD (between 0.1% and 0.005%)
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
PMID 29543232- Detected in one proband with features of MFS, who also carried a pathogenic FBN1 variant: c.3193delG p.Glu1065LysfsTer23, however phasing not provided.
BP4
In silico tools are conflicting. REVEL score: 0.375 CADD score: 1.98 MetaLR score: 0.51
Approved on: 2023-06-15
Published on: 2023-06-15
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