NM_000138.5:c.3454G>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM1PP2BP6BS2
The NM_000138.5(FBN1):c.3454G>A(p.Ala1152Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000564 in 1,614,192 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000138.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152190Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251472Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135914
GnomAD4 exome AF: 0.0000458 AC: 67AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.0000454 AC XY: 33AN XY: 727248
GnomAD4 genome AF: 0.000158 AC: 24AN: 152308Hom.: 1 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74460
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Uncertain:1Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
This missense variant replaces alanine with threonine at codon 1152 of the FBN1 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with thoracic aortic aneurysm and dissection with penetrating atherosclerotic ulcers (PMID: 29543232). This variant has been identified in 14/282878 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Marfan syndrome;C0265287:Acromicric dysplasia;C1858556:MASS syndrome;C1861456:Stiff skin syndrome;C1869115:Weill-Marchesani syndrome 2, dominant;C3280054:Geleophysic dysplasia 2;C3541518:Ectopia lentis 1, isolated, autosomal dominant;C4310796:Progeroid and marfanoid aspect-lipodystrophy syndrome Uncertain:1Benign:1
This variant has been reported in the literature in one individual with TAAD (Weerakkody 2018 PMID: 29543232). This variant is present in the Genome Aggregation Database (Highest reported MAF: 0.04% [6/15284], and in 1 homozygote; https://gnomad.broadinstitute.org/variant/15-48487321-C-T?dataset=gnomad_r3). It is also present in ClinVar, with classifications ranging from uncertain significance to likely benign (Variation ID: 255292). Evolutionary conservation and computational prediction tools are unclear for this variant. In summary, data on this variant suggests that this variant does not cause disease but requires further evidence. Therefore, this variant is classified as likely benign. -
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not specified Benign:2
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Variant summary: FBN1 c.3454G>A (p.Ala1152Thr) results in a non-conservative amino acid change located in the EGF-like domain (IPR000742) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 5.6e-05 in 1614192 control chromosomes, predominantly at a frequency of 0.00023 within the African or African-American subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 2-fold of the estimated maximal expected allele frequency for a pathogenic variant in FBN1 causing Marfan Syndrome phenotype (0.00011). c.3454G>A has been reported in the literature as a VUS in a setting of multigene panel testing in an individual from a large cohort of familial and sporadic cases of aneurysm or dissection of the thoracic aorta (Weerakkody_2018). This report does not provide unequivocal conclusions about association of the variant with Marfan Syndrome or other FBN1-related disorders. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 29543232). ClinVar contains an entry for this variant (Variation ID: 255292). Based on the evidence outlined above, the variant was classified as likely benign. -
Marfan syndrome Uncertain:1
This missense variant replaces alanine with threonine at codon 1152 of the FBN1 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with thoracic aortic aneurysm and dissection with penetrating atherosclerotic ulcers (PMID: 29543232). This variant has been identified in 14/282878 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
not provided Uncertain:1
Has been reported as a variant of uncertain significance in an individual with TAAD (Weerakkody et al., 2018); In silico analysis supports that this missense variant does not alter protein structure/function; Although located in a calcium-binding EGF-like domain of the FBN1 gene, it does not affect a cysteine residue within this domain; cysteine substitutions in the calcium-binding EGF-like domains represent the majority of pathogenic missense changes associated with FBN1-related disorders (Collod-Beroud et al., 2003); Reported in ClinVar (ClinVar Variant ID# 255292; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 27535533, 26582918, 29543232) -
Marfan syndrome;C4707243:Familial thoracic aortic aneurysm and aortic dissection Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at