rs12162237
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032447.5(FBN3):c.542-49C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 1,484,270 control chromosomes in the GnomAD database, including 181,385 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.53 ( 22400 hom., cov: 32)
Exomes 𝑓: 0.48 ( 158985 hom. )
Consequence
FBN3
NM_032447.5 intron
NM_032447.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0340
Genes affected
FBN3 (HGNC:18794): (fibrillin 3) This gene encodes a memebr of the fibrillin protein family. Fibrillins are extracellular matrix molecules that assemble into microfibrils in many connective tissues. This gene is most highly expressed in fetal tissues and its protein product is localized to extracellular microfibrils of developing skeletal elements, skin, lung, kidney, and skeletal muscle. This gene is potentially involved in Weill-Marchesani syndrome. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBN3 | NM_032447.5 | c.542-49C>T | intron_variant | ENST00000600128.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBN3 | ENST00000600128.6 | c.542-49C>T | intron_variant | 1 | NM_032447.5 | ||||
FBN3 | ENST00000270509.6 | c.542-49C>T | intron_variant | 1 | |||||
FBN3 | ENST00000601739.5 | c.542-49C>T | intron_variant | 1 | |||||
FBN3 | ENST00000651877.1 | c.542-49C>T | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.535 AC: 81240AN: 151940Hom.: 22372 Cov.: 32
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GnomAD3 exomes AF: 0.531 AC: 86682AN: 163326Hom.: 23336 AF XY: 0.535 AC XY: 47375AN XY: 88610
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GnomAD4 exome AF: 0.485 AC: 645915AN: 1332212Hom.: 158985 Cov.: 21 AF XY: 0.490 AC XY: 322560AN XY: 657818
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GnomAD4 genome ? AF: 0.535 AC: 81326AN: 152058Hom.: 22400 Cov.: 32 AF XY: 0.537 AC XY: 39922AN XY: 74312
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at