Genetic Variant NM_002271.6:c.364+64delT (chr13-97985663-CT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_002271.6(IPO5):c.364+64delT 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 0.54 ( 21645 hom., cov: 0)

Exomes 𝑓: 0.47 ( 30311 hom. )

Failed GnomAD Quality Control

Consequence

IPO5
NM_002271.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76

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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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IPO5	NM_002271.6 link	c.364+64delT		intron_variant	Intron 6 of 28	ENST00000651721.2	NP_002262.4	O00410-1Q9BVS9B3KWG6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IPO5	ENST00000651721.2 link	c.364+51delT		intron_variant	Intron 6 of 28		NM_002271.6	ENSP00000499125.1		O00410-1

Frequencies

GnomAD3 genomes

AF:

0.544

AC:

79192

AN:

145584

Hom.:

21627

Cov.:

show subpopulations

Gnomad AFR

AF:

0.682

Gnomad AMI

AF:

0.474

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.454

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.451

Gnomad FIN

AF:

0.512

Gnomad MID

AF:

0.431

Gnomad NFE

AF:

0.526

Gnomad OTH

AF:

0.492

GnomAD2 exomes

AF:

0.511

AC:

66601

AN:

130350

AF XY:

0.514

show subpopulations

Gnomad AFR exome

AF:

0.543

Gnomad AMR exome

AF:

0.462

Gnomad ASJ exome

AF:

0.497

Gnomad EAS exome

AF:

0.386

Gnomad FIN exome

AF:

0.536

Gnomad NFE exome

AF:

0.537

Gnomad OTH exome

AF:

0.503

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.466

AC:

356828

AN:

765850

Hom.:

30311

Cov.:

AF XY:

0.467

AC XY:

185961

AN XY:

398000

show subpopulations

African (AFR)

AF:

0.482

AC:

8053

AN:

16710

American (AMR)

AF:

0.415

AC:

11711

AN:

28212

Ashkenazi Jewish (ASJ)

AF:

0.449

AC:

8115

AN:

18072

East Asian (EAS)

AF:

0.366

AC:

11242

AN:

30720

South Asian (SAS)

AF:

0.450

AC:

25591

AN:

56870

European-Finnish (FIN)

AF:

0.478

AC:

20636

AN:

43190

Middle Eastern (MID)

AF:

0.427

AC:

1375

AN:

3222

European-Non Finnish (NFE)

AF:

0.476

AC:

253778

AN:

533582

Other (OTH)

AF:

0.463

AC:

16327

AN:

35272

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

9385

18771

28156

37542

46927

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6252

12504

18756

25008

31260

<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:

0.544

AC:

79233

AN:

145638

Hom.:

21645

Cov.:

AF XY:

0.539

AC XY:

38106

AN XY:

70640

show subpopulations

African (AFR)

AF:

0.682

AC:

27063

AN:

39708

American (AMR)

AF:

0.439

AC:

6355

AN:

14486

Ashkenazi Jewish (ASJ)

AF:

0.454

AC:

1534

AN:

3380

East Asian (EAS)

AF:

0.227

AC:

1107

AN:

4868

South Asian (SAS)

AF:

0.451

AC:

2054

AN:

4554

European-Finnish (FIN)

AF:

0.512

AC:

4736

AN:

9258

Middle Eastern (MID)

AF:

0.435

AC:

121

AN:

278

European-Non Finnish (NFE)

AF:

0.526

AC:

34861

AN:

66216

Other (OTH)

AF:

0.490

AC:

990

AN:

2020

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.521

Heterozygous variant carriers

1763

3526

5290

7053

8816

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.317

Hom.:

584

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over