rs780989245
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS2
The NM_001999.4(FBN2):c.5567A>G(p.Asn1856Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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. N1856K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001999.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBN2 | NM_001999.4 | c.5567A>G | p.Asn1856Ser | missense_variant | 44/65 | ENST00000262464.9 | |
FBN2 | XM_017009228.3 | c.5414A>G | p.Asn1805Ser | missense_variant | 43/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBN2 | ENST00000262464.9 | c.5567A>G | p.Asn1856Ser | missense_variant | 44/65 | 1 | NM_001999.4 | P1 | |
FBN2 | ENST00000703783.1 | n.2351A>G | non_coding_transcript_exon_variant | 19/38 | |||||
FBN2 | ENST00000703785.1 | n.2270A>G | non_coding_transcript_exon_variant | 18/27 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251260Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135778
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461738Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727174
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
Congenital contractural arachnodactyly Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at