rs2276737
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_003571.4(BFSP2):c.603G>A(p.Ala201=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 1,613,420 control chromosomes in the GnomAD database, including 282,437 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.47 ( 19696 hom., cov: 32)
Exomes 𝑓: 0.59 ( 262741 hom. )
Consequence
BFSP2
NM_003571.4 synonymous
NM_003571.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.161
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 Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 3-133448519-G-A is Benign according to our data. Variant chr3-133448519-G-A is described in ClinVar as [Benign]. Clinvar id is 1164247.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-133448519-G-A is described in Lovd as [Benign]. Variant chr3-133448519-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=0.161 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BFSP2 | NM_003571.4 | c.603G>A | p.Ala201= | synonymous_variant | 3/7 | ENST00000302334.3 | |
BFSP2-AS1 | NR_135277.1 | n.381-2944C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BFSP2 | ENST00000302334.3 | c.603G>A | p.Ala201= | synonymous_variant | 3/7 | 1 | NM_003571.4 | P1 | |
BFSP2-AS1 | ENST00000515542.1 | n.282+262C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.469 AC: 71279AN: 151912Hom.: 19695 Cov.: 32
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GnomAD3 exomes AF: 0.539 AC: 135182AN: 251004Hom.: 38870 AF XY: 0.557 AC XY: 75611AN XY: 135658
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GnomAD4 exome AF: 0.593 AC: 866158AN: 1461388Hom.: 262741 Cov.: 54 AF XY: 0.596 AC XY: 433386AN XY: 727040
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GnomAD4 genome ? AF: 0.469 AC: 71287AN: 152032Hom.: 19696 Cov.: 32 AF XY: 0.468 AC XY: 34779AN XY: 74316
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cataract 12 multiple types Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at