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.4583-5A>G

CA16614422

406332 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 73ca8855-9682-4983-8b82-6adb0367e0ef

HGVS expressions

NM_000138.5:c.4583-5A>G
NM_000138.5(FBN1):c.4583-5A>G
NC_000015.10:g.48468107T>C
CM000677.2:g.48468107T>C
NC_000015.9:g.48760304T>C
CM000677.1:g.48760304T>C
NC_000015.8:g.46547596T>C
NG_008805.2:g.182682A>G
ENST00000684448.1:n.3257-5A>G
ENST00000316623.10:c.4583-5A>G
ENST00000316623.9:c.4583-5A>G
ENST00000537463.6:c.*346-5A>G
NM_000138.4:c.4583-5A>G

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP4 PP3 PS4_Moderate PM6_Supporting
Not Met criteria codes 21
PS3 PS1 PS2 BA1 PP1 PP2 PM5 PM1 PM3 PM4 PVS1 BS3 BS4 BS1 BS2 BP5 BP7 BP2 BP3 BP4 BP1

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_000138.5 c.4583-5A>G variant in FBN1 is a variant in the splice acceptor region of intron 37. Computational splice prediction algorithms predict that this variant impacts splicing (PP3). This variant was identified in the literature and public databases in two individuals with clinical diagnoses of Marfan syndrome including once as de novo in an individual with phenotype consistent with but not highly specific to FBN1 and in an individual with aortic aneurysm and other features suggestive of Marfan syndrome; it was also found to segregate with disease in at least one affected family member (PS4_moderate, PM6_supporting; PMID: 25101912, Invitae internal data, ClinVar ID: 406332). It was also identified in a third individual with a clinical diagnosis of Marfan syndrome (PP4; Johns Hopkins). This variant is not present in gnomAD v2.1.1 or v3.1.2 (PM2_supporting; https://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as likely pathogenic for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP (PS4_moderate, PM2_supporting, PM6_supporting, PP3, PP4).
Met criteria codes
PM2_Supporting
not present in gnomAD v2.1.1 or v3.1.2
PP4
1 internal proband who meets revised Ghent criteria (Johns Hopkins)
PP3
GeneSplicer, MaxEntscan, and NNSPLICE all predict addition/strengthening of cryptic acceptor site, and weakening of canonical acceptor site; SpliceAI score for Acceptor Gain = 0.99
PS4_Moderate
2 probands who meet revised Ghent criteria, 1 with TAAD + skeletal features; 2.5 PS4 points
PM6_Supporting
1 proband (Baudhuin et al) identified to have this variant as de novo (mat/pat not confirmed) with consistent but not highly specific phenotype
Not Met criteria codes
PS3
no evidence
PS1
n/a
PS2
no evidence
BA1
PM2_supporting
PP1
only 1 segregation
PP2
n/a
PM5
n/a
PM1
n/a
PM3
n/a for FBN1
PM4
n/a
PVS1
n/a
BS3
no evidence
BS4
no evidence
BS1
PM2_supporting
BS2
n/a for FBN1
BP5
no evidence
BP7
n/a
BP2
no evidence
BP3
n/a for FBN1
BP4
PP3 met
BP1
n/a for FBN1
Approved on: 2023-06-15
Published on: 2023-06-15
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