Genetic Variant IPO5:c.1716+24_1716+44dupTTTTTTTTTTTTTTTTTTTTT (chr13-98006356-A-ATTTTTTTTTTTTTTTTTTTTT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_002271.6(IPO5):c.1716+24_1716+44dupTTTTTTTTTTTTTTTTTTTTT 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 INS_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 0.000080 ( 1 hom., cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

IPO5
NM_002271.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00500

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]

IPO5 links:

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new If you want to explore the variant's impact on the transcript NM_002271.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IPO5	NM_002271.6	MANE Select	c.1716+24_1716+44dupTTTTTTTTTTTTTTTTTTTTT		intron	N/A	NP_002262.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IPO5	ENST00000651721.2	MANE Select	c.1716+8_1716+9insTTTTTTTTTTTTTTTTTTTTT	intron	N/A	ENSP00000499125.1	O00410-1
IPO5	ENST00000261574.10	TSL:1	c.1770+8_1770+9insTTTTTTTTTTTTTTTTTTTTT	intron	N/A	ENSP00000261574.5	O00410-3
IPO5	ENST00000490680.5	TSL:1	c.1716+8_1716+9insTTTTTTTTTTTTTTTTTTTTT	intron	N/A	ENSP00000418393.1	O00410-1

Frequencies

GnomAD3 genomes

AF:

0.0000796

AC:

AN:

62852

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000432

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

494016

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

261218

African (AFR)

AF:

0.00

AC:

AN:

5718

American (AMR)

AF:

0.00

AC:

AN:

17606

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10956

East Asian (EAS)

AF:

0.00

AC:

AN:

18820

South Asian (SAS)

AF:

0.00

AC:

AN:

47976

European-Finnish (FIN)

AF:

0.00

AC:

AN:

28170

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2856

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

340596

Other (OTH)

AF:

0.00

AC:

AN:

21318

GnomAD4 genome

AF:

0.0000795

AC:

AN:

62862

Hom.:

Cov.:

AF XY:

0.0000710

AC XY:

AN XY:

28162

show subpopulations

African (AFR)

AF:

0.000431

AC:

AN:

11604

American (AMR)

AF:

0.00

AC:

AN:

4474

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2148

East Asian (EAS)

AF:

0.00

AC:

AN:

2448

South Asian (SAS)

AF:

0.00

AC:

AN:

1886

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1706

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

37134

Other (OTH)

AF:

0.00

AC:

AN:

830

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.0050

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

13-98006356-ATTTTTTTTTTTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over