rs74108123
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002271.6(IPO5):c.3065+21C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00371 in 1,510,478 control chromosomes in the GnomAD database, including 143 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 0.019 ( 85 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 58 hom. )
Consequence
IPO5
NM_002271.6 intron
NM_002271.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.04
Genes affected
IPO5 (HGNC:6402): (importin 5) Nucleocytoplasmic transport, a signal- and energy-dependent process, takes place through nuclear pore complexes embedded in the nuclear envelope. The import of proteins containing a nuclear localization signal (NLS) requires the NLS import receptor, a heterodimer of importin alpha and beta subunits also known as karyopherins. Importin alpha binds the NLS-containing cargo in the cytoplasm and importin beta docks the complex at the cytoplasmic side of the nuclear pore complex. In the presence of nucleoside triphosphates and the small GTP binding protein Ran, the complex moves into the nuclear pore complex and the importin subunits dissociate. Importin alpha enters the nucleoplasm with its passenger protein and importin beta remains at the pore. Interactions between importin beta and the FG repeats of nucleoporins are essential in translocation through the pore complex. The protein encoded by this gene is a member of the importin beta family. [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=-0.77).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0629 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IPO5 | NM_002271.6 | c.3065+21C>T | intron_variant | ENST00000651721.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IPO5 | ENST00000651721.2 | c.3065+21C>T | intron_variant | NM_002271.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0188 AC: 2863AN: 152118Hom.: 85 Cov.: 32
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GnomAD3 exomes AF: 0.00523 AC: 1307AN: 249674Hom.: 32 AF XY: 0.00375 AC XY: 506AN XY: 135090
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GnomAD4 exome AF: 0.00201 AC: 2735AN: 1358242Hom.: 58 Cov.: 21 AF XY: 0.00168 AC XY: 1147AN XY: 681410
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GnomAD4 genome ? AF: 0.0188 AC: 2865AN: 152236Hom.: 85 Cov.: 32 AF XY: 0.0176 AC XY: 1312AN XY: 74424
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at