13-98006356-ATTTTTTTTTTTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_002271.6(IPO5):​c.1716+38_1716+44dupTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00051 ( 6 hom., cov: 0)
Exomes 𝑓: 0.00019 ( 2 hom. )
Failed GnomAD Quality Control

Consequence

IPO5
NM_002271.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00500
Variant links:
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 Likely_benign. Variant got -4 ACMG points.

BS2
High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IPO5NM_002271.6 linkc.1716+38_1716+44dupTTTTTTT intron_variant Intron 17 of 28 ENST00000651721.2 NP_002262.4 O00410-1Q9BVS9B3KWG6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IPO5ENST00000651721.2 linkc.1716+8_1716+9insTTTTTTT intron_variant Intron 17 of 28 NM_002271.6 ENSP00000499125.1 O00410-1

Frequencies

GnomAD3 genomes
AF:
0.000509
AC:
32
AN:
62854
Hom.:
6
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00147
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000224
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000811
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000296
Gnomad OTH
AF:
0.00122
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000186
AC:
92
AN:
493980
Hom.:
2
Cov.:
0
AF XY:
0.000226
AC XY:
59
AN XY:
261196
show subpopulations
Gnomad4 AFR exome
AF:
0.000175
Gnomad4 AMR exome
AF:
0.0000568
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000319
Gnomad4 SAS exome
AF:
0.000855
Gnomad4 FIN exome
AF:
0.0000710
Gnomad4 NFE exome
AF:
0.000115
Gnomad4 OTH exome
AF:
0.0000938
GnomAD4 genome
AF:
0.000509
AC:
32
AN:
62862
Hom.:
6
Cov.:
0
AF XY:
0.000568
AC XY:
16
AN XY:
28162
show subpopulations
Gnomad4 AFR
AF:
0.00146
Gnomad4 AMR
AF:
0.000224
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000817
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000296
Gnomad4 OTH
AF:
0.00121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs568589408; hg19: chr13-98658610; API