rs2023224
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001195.5(BFSP1):c.439-2308C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 803,654 control chromosomes in the GnomAD database, including 61,488 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 0.41 ( 12910 hom., cov: 33)
Exomes 𝑓: 0.38 ( 48578 hom. )
Consequence
BFSP1
NM_001195.5 intron
NM_001195.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.789
Genes affected
BFSP1 (HGNC:1040): (beaded filament structural protein 1) This gene encodes a lens-specific intermediate filament-like protein named filensin. The encoded protein is expressed in lens fiber cells after differentiation has begun. This protein functions as a component of the beaded filament which is a cytoskeletal structure found in lens fiber cells. Mutations in this gene are the cause of autosomal recessive cortical juvenile-onset cataract. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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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=-0.61).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BFSP1 | NM_001195.5 | c.439-2308C>T | intron_variant | ENST00000377873.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BFSP1 | ENST00000377873.8 | c.439-2308C>T | intron_variant | 1 | NM_001195.5 | P1 | |||
RPS27AP2 | ENST00000457576.1 | n.282G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.408 AC: 61938AN: 151944Hom.: 12879 Cov.: 33
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GnomAD4 exome AF: 0.383 AC: 249469AN: 651592Hom.: 48578 Cov.: 7 AF XY: 0.384 AC XY: 135901AN XY: 353788
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GnomAD4 genome ? AF: 0.408 AC: 62016AN: 152062Hom.: 12910 Cov.: 33 AF XY: 0.407 AC XY: 30228AN XY: 74320
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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