chr22-35761272-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001349999.2(RBFOX2):c.894G>A(p.Val298=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000562 in 1,614,102 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00037 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00058 ( 1 hom. )
Consequence
RBFOX2
NM_001349999.2 synonymous
NM_001349999.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.537
Genes affected
RBFOX2 (HGNC:9906): (RNA binding fox-1 homolog 2) This gene is one of several human genes similar to the C. elegans gene Fox-1. This gene encodes an RNA binding protein that is thought to be a key regulator of alternative exon splicing in the nervous system and other cell types. The protein binds to a conserved UGCAUG element found downstream of many alternatively spliced exons and promotes inclusion of the alternative exon in mature transcripts. The protein also interacts with the estrogen receptor 1 transcription factor and regulates estrogen receptor 1 transcriptional activity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 22-35761272-C-T is Benign according to our data. Variant chr22-35761272-C-T is described in ClinVar as [Benign]. Clinvar id is 1640226.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.537 with no splicing effect.
BS2
High AC in GnomAd4 at 57 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBFOX2 | NM_001349999.2 | c.894G>A | p.Val298= | synonymous_variant | 9/14 | ENST00000695854.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBFOX2 | ENST00000695854.1 | c.894G>A | p.Val298= | synonymous_variant | 9/14 | NM_001349999.2 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000375 AC: 57AN: 152110Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000665 AC: 167AN: 251226Hom.: 1 AF XY: 0.000707 AC XY: 96AN XY: 135772
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GnomAD4 exome AF: 0.000581 AC: 850AN: 1461874Hom.: 1 Cov.: 33 AF XY: 0.000619 AC XY: 450AN XY: 727234
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GnomAD4 genome AF: 0.000374 AC: 57AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74434
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at