rs1010471
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005087.4(FXR1):c.1604-2009G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,016 control chromosomes in the GnomAD database, including 21,461 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 0.50 ( 21461 hom., cov: 33)
Consequence
FXR1
NM_005087.4 intron
NM_005087.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.02
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FXR1 | NM_005087.4 | c.1604-2009G>A | intron_variant | ENST00000357559.9 | |||
FXR1 | NM_001013438.3 | c.1604-2818G>A | intron_variant | ||||
FXR1 | NM_001013439.3 | c.1349-2009G>A | intron_variant | ||||
FXR1 | NM_001363882.1 | c.1349-2818G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FXR1 | ENST00000357559.9 | c.1604-2009G>A | intron_variant | 1 | NM_005087.4 |
Frequencies
GnomAD3 genomes ? AF: 0.496 AC: 75410AN: 151900Hom.: 21400 Cov.: 33
GnomAD3 genomes
?
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151900
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.497 AC: 75531AN: 152016Hom.: 21461 Cov.: 33 AF XY: 0.492 AC XY: 36591AN XY: 74302
GnomAD4 genome
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75531
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33
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36591
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74302
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2003
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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