rs3910564
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_006390.4(IPO8):c.2268+1718A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 28)
Failed GnomAD Quality Control
Consequence
IPO8
NM_006390.4 intron
NM_006390.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.66
Genes affected
IPO8 (HGNC:9853): (importin 8) The importin-alpha/beta complex and the GTPase Ran mediate nuclear import of proteins with a classical nuclear localization signal. The protein encoded by this gene is a member of a class of approximately 20 potential Ran targets that share a sequence motif related to the Ran-binding site of importin-beta. This protein binds to the nuclear pore complex and, along with RanGTP and RANBP1, inhibits the GAP stimulation of the Ran GTPase. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IPO8 | NM_006390.4 | c.2268+1718A>T | intron_variant | ENST00000256079.9 | |||
IPO8 | NM_001190995.2 | c.1653+1718A>T | intron_variant | ||||
IPO8 | XM_017018691.3 | c.2217+1718A>T | intron_variant | ||||
IPO8 | XM_017018692.2 | c.2082+1718A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IPO8 | ENST00000256079.9 | c.2268+1718A>T | intron_variant | 1 | NM_006390.4 | P1 | |||
IPO8 | ENST00000544829.5 | c.1653+1718A>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 151458Hom.: 0 Cov.: 28 FAILED QC
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151458Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 73890
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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