rs104893685
Positions:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP6_ModerateBP7
The NM_003571.4(BFSP2):c.859C>A(p.Arg287Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,838 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
BFSP2
NM_003571.4 synonymous
NM_003571.4 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 1.62
Genes affected
BFSP2 (HGNC:1041): (beaded filament structural protein 2) More than 99% of the vertebrate ocular lens is comprised of terminally differentiated lens fiber cells. Two lens-specific intermediate filament-like proteins, the protein product of this gene (phakinin), and filensin, are expressed only after fiber cell differentiation has begun. Both proteins are found in a structurally unique cytoskeletal element that is referred to as the beaded filament (BF). Mutations in this gene have been associated with juvenile-onset, progressive cataracts and Dowling-Meara epidermolysis bullosa simplex. [provided by RefSeq, Jun 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 3-133450432-C-A is Benign according to our data. Variant chr3-133450432-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1571023.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.62 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BFSP2 | NM_003571.4 | c.859C>A | p.Arg287Arg | synonymous_variant | 4/7 | ENST00000302334.3 | NP_003562.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BFSP2 | ENST00000302334.3 | c.859C>A | p.Arg287Arg | synonymous_variant | 4/7 | 1 | NM_003571.4 | ENSP00000304987.2 | ||
BFSP2-AS1 | ENST00000515542.1 | n.168-1537G>T | intron_variant | 1 | ||||||
BFSP2 | ENST00000510039.1 | n.10C>A | non_coding_transcript_exon_variant | 1/4 | 3 | |||||
BFSP2 | ENST00000511434.1 | n.325C>A | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
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31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251152Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135736
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727220
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GnomAD4 genome Cov.: 31
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cataract 12 multiple types Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 08, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Uncertain
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