rs1338036259
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The ENST00000262464.9(FBN2):āc.2271T>Cā(p.Ser757=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000748 in 1,605,322 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 Benign (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.0000076 ( 0 hom. )
Consequence
FBN2
ENST00000262464.9 synonymous
ENST00000262464.9 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.602
Genes affected
FBN2 (HGNC:3604): (fibrillin 2) The protein encoded by this gene is a component of connective tissue microfibrils and may be involved in elastic fiber assembly. Mutations in this gene cause congenital contractural arachnodactyly. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 5-128366408-A-G is Benign according to our data. Variant chr5-128366408-A-G is described in ClinVar as [Benign]. Clinvar id is 458741.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.602 with no splicing effect.
BS2
High AC in GnomAdExome4 at 11 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FBN2 | NM_001999.4 | c.2271T>C | p.Ser757= | synonymous_variant | 17/65 | ENST00000262464.9 | NP_001990.2 | |
FBN2 | XM_017009228.3 | c.2118T>C | p.Ser706= | synonymous_variant | 16/64 | XP_016864717.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBN2 | ENST00000262464.9 | c.2271T>C | p.Ser757= | synonymous_variant | 17/65 | 1 | NM_001999.4 | ENSP00000262464 | P1 | |
FBN2 | ENST00000508989.5 | c.2172T>C | p.Ser724= | synonymous_variant | 16/33 | 2 | ENSP00000425596 | |||
FBN2 | ENST00000511489.1 | n.492T>C | non_coding_transcript_exon_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250120Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135226
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GnomAD4 exome AF: 0.00000757 AC: 11AN: 1453222Hom.: 0 Cov.: 26 AF XY: 0.00000968 AC XY: 7AN XY: 723306
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74296
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital contractural arachnodactyly Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 16, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at