chr5-128278775-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 1P and 11B. PP2BP4_ModerateBP6BS1BS2
The NM_001999.4(FBN2):c.7205G>A(p.Arg2402His) variant causes a missense change. The variant allele was found at a frequency of 0.000105 in 1,614,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2402C) has been classified as Likely benign.
Frequency
Consequence
NM_001999.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBN2 | NM_001999.4 | c.7205G>A | p.Arg2402His | missense_variant | 57/65 | ENST00000262464.9 | |
FBN2 | XM_017009228.3 | c.7052G>A | p.Arg2351His | missense_variant | 56/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBN2 | ENST00000262464.9 | c.7205G>A | p.Arg2402His | missense_variant | 57/65 | 1 | NM_001999.4 | P1 | |
FBN2 | ENST00000703783.1 | n.3989G>A | non_coding_transcript_exon_variant | 32/38 |
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000139 AC: 35AN: 251022Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135644
GnomAD4 exome AF: 0.0000841 AC: 123AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.0000660 AC XY: 48AN XY: 727208
GnomAD4 genome AF: 0.000302 AC: 46AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 27, 2014 | - - |
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2020 | 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 23, 2021 | - - |
Congenital contractural arachnodactyly Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at