rs4596126
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001004019.2(FBLN2):c.1939+112A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 951,736 control chromosomes in the GnomAD database, including 44,859 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 0.39 ( 17009 hom., cov: 33)
Exomes 𝑓: 0.24 ( 27850 hom. )
Consequence
FBLN2
NM_001004019.2 intron
NM_001004019.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.93
Genes affected
FBLN2 (HGNC:3601): (fibulin 2) This gene encodes an extracellular matrix protein, which belongs to the fibulin family. This protein binds various extracellular ligands and calcium. It may play a role during organ development, in particular, during the differentiation of heart, skeletal and neuronal structures. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FBLN2 | NM_001004019.2 | c.1939+112A>C | intron_variant | ENST00000404922.8 | NP_001004019.1 | |||
SNORA93 | NR_132775.1 | n.17A>C | non_coding_transcript_exon_variant | 1/1 | ||||
FBLN2 | NM_001165035.2 | c.1939+112A>C | intron_variant | NP_001158507.1 | ||||
FBLN2 | NM_001998.3 | c.1939+112A>C | intron_variant | NP_001989.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBLN2 | ENST00000404922.8 | c.1939+112A>C | intron_variant | 5 | NM_001004019.2 | ENSP00000384169 | P1 | |||
FBLN2 | ENST00000295760.11 | c.1939+112A>C | intron_variant | 1 | ENSP00000295760 | |||||
FBLN2 | ENST00000492059.5 | c.1939+112A>C | intron_variant | 2 | ENSP00000420042 | P1 | ||||
FBLN2 | ENST00000477845.1 | n.477+112A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.392 AC: 59612AN: 152092Hom.: 16957 Cov.: 33
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GnomAD4 exome AF: 0.243 AC: 193914AN: 799526Hom.: 27850 AF XY: 0.242 AC XY: 98268AN XY: 406698
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GnomAD4 genome AF: 0.392 AC: 59724AN: 152210Hom.: 17009 Cov.: 33 AF XY: 0.388 AC XY: 28843AN XY: 74432
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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