GeneBe

rs568589408

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_002271.6(IPO5):​c.1716+21_1716+44delTTTTTTTTTTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000032 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000026 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

IPO5
NM_002271.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.30

Publications

0 publications found
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 was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002271.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
IPO5
NM_002271.6
MANE Select
c.1716+21_1716+44delTTTTTTTTTTTTTTTTTTTTTTTT
intron
N/ANP_002262.4

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
IPO5
ENST00000651721.2
MANE Select
c.1716+9_1716+32delTTTTTTTTTTTTTTTTTTTTTTTT
intron
N/AENSP00000499125.1O00410-1
IPO5
ENST00000261574.10
TSL:1
c.1770+9_1770+32delTTTTTTTTTTTTTTTTTTTTTTTT
intron
N/AENSP00000261574.5O00410-3
IPO5
ENST00000490680.5
TSL:1
c.1716+9_1716+32delTTTTTTTTTTTTTTTTTTTTTTTT
intron
N/AENSP00000418393.1O00410-1

Frequencies

GnomAD3 genomes
AF:
0.0000318
AC:
2
AN:
62854
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000538
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000263
AC:
13
AN:
494018
Hom.:
0
AF XY:
0.0000230
AC XY:
6
AN XY:
261220
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
5718
American (AMR)
AF:
0.00
AC:
0
AN:
17606
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
10956
East Asian (EAS)
AF:
0.00
AC:
0
AN:
18822
South Asian (SAS)
AF:
0.00
AC:
0
AN:
47976
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
28170
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2856
European-Non Finnish (NFE)
AF:
0.0000382
AC:
13
AN:
340596
Other (OTH)
AF:
0.00
AC:
0
AN:
21318
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.702
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0000318
AC:
2
AN:
62854
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
28156
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
11582
American (AMR)
AF:
0.00
AC:
0
AN:
4464
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2148
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2466
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1890
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
1706
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
92
European-Non Finnish (NFE)
AF:
0.0000538
AC:
2
AN:
37142
Other (OTH)
AF:
0.00
AC:
0
AN:
820
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
53

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.3

Splicing

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

Publications

Other links and lift over

dbSNP: rs568589408; hg19: chr13-98658610; API
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