rs779567163
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP6_ModerateBS2
The NM_001999.4(FBN2):c.5639C>T(p.Ala1880Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,614,026 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1880T) has been classified as Likely benign.
Frequency
Consequence
NM_001999.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBN2 | NM_001999.4 | c.5639C>T | p.Ala1880Val | missense_variant | 44/65 | ENST00000262464.9 | |
FBN2 | XM_017009228.3 | c.5486C>T | p.Ala1829Val | missense_variant | 43/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBN2 | ENST00000262464.9 | c.5639C>T | p.Ala1880Val | missense_variant | 44/65 | 1 | NM_001999.4 | P1 | |
FBN2 | ENST00000703783.1 | n.2423C>T | non_coding_transcript_exon_variant | 19/38 | |||||
FBN2 | ENST00000703785.1 | n.2342C>T | non_coding_transcript_exon_variant | 18/27 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251336Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135816
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461756Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727180
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74454
ClinVar
Submissions by phenotype
Congenital contractural arachnodactyly Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at