3-180971145-TAGAC-T
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_005087.4(FXR1):c.1603+790_1603+793delACAG variant causes a intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000539 in 1,113,656 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000054 ( 0 hom. )
Consequence
FXR1
NM_005087.4 intron
NM_005087.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.79
Genes affected
FXR1 (HGNC:4023): (FMR1 autosomal homolog 1) The protein encoded by this gene is an RNA binding protein that interacts with the functionally-similar proteins FMR1 and FXR2. These proteins shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Three 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 Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-180971145-TAGAC-T is Pathogenic according to our data. Variant chr3-180971145-TAGAC-T is described in ClinVar as [Pathogenic]. Clinvar id is 828056.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-180971145-TAGAC-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FXR1 | NM_005087.4 | c.1603+790_1603+793delACAG | intron_variant | ENST00000357559.9 | NP_005078.2 | |||
FXR1 | NM_001013438.3 | c.1603+790_1603+793delACAG | intron_variant | NP_001013456.1 | ||||
FXR1 | NM_001013439.3 | c.1348+790_1348+793delACAG | intron_variant | NP_001013457.1 | ||||
FXR1 | NM_001363882.1 | c.1348+790_1348+793delACAG | intron_variant | NP_001350811.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FXR1 | ENST00000357559.9 | c.1603+790_1603+793delACAG | intron_variant | 1 | NM_005087.4 | ENSP00000350170.3 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 genomes
Cov.:
30
GnomAD4 exome AF: 0.00000539 AC: 6AN: 1113656Hom.: 0 AF XY: 0.00000732 AC XY: 4AN XY: 546452
GnomAD4 exome
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1113656
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4
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546452
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GnomAD4 genome Cov.: 30
GnomAD4 genome
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30
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Myopathy, congenital, with respiratory insufficiency and bone fractures Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 16, 2024 | - - |
Computational scores
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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