Variant rs633161 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002271.6(IPO5):c.1498-26G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 1,467,068 control chromosomes in the GnomAD database, including 246,574 homozygotes. 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 0.63 ( 31776 hom., cov: 31)

Exomes 𝑓: 0.57 ( 214798 hom. )

Consequence

IPO5
NM_002271.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0710

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IPO5	NM_002271.6 linkuse as main transcript	c.1498-26G>A		intron_variant		ENST00000651721.2	NP_002262.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IPO5	ENST00000651721.2 linkuse as main transcript	c.1498-26G>A		intron_variant			NM_002271.6	ENSP00000499125	P1	O00410-1

Frequencies

GnomAD3 genomes

AF:

0.631

AC:

95789

AN:

151862

Hom.:

31717

Cov.:

show subpopulations

Gnomad AFR

AF:

0.855

Gnomad AMI

AF:

0.594

Gnomad AMR

AF:

0.477

Gnomad ASJ

AF:

0.508

Gnomad EAS

AF:

0.561

Gnomad SAS

AF:

0.602

Gnomad FIN

AF:

0.538

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.559

Gnomad OTH

AF:

0.571

GnomAD3 exomes

AF:

0.550

AC:

136375

AN:

247806

Hom.:

39007

AF XY:

0.552

AC XY:

73995

AN XY:

134034

show subpopulations

Gnomad AFR exome

AF:

0.861

Gnomad AMR exome

AF:

0.376

Gnomad ASJ exome

AF:

0.507

Gnomad EAS exome

AF:

0.536

Gnomad SAS exome

AF:

0.595

Gnomad FIN exome

AF:

0.527

Gnomad NFE exome

AF:

0.558

Gnomad OTH exome

AF:

0.528

GnomAD4 exome

AF:

0.567

AC:

746228

AN:

1315088

Hom.:

214798

Cov.:

AF XY:

0.569

AC XY:

376423

AN XY:

662020

show subpopulations

Gnomad4 AFR exome

AF:

0.866

Gnomad4 AMR exome

AF:

0.387

Gnomad4 ASJ exome

AF:

0.512

Gnomad4 EAS exome

AF:

0.545

Gnomad4 SAS exome

AF:

0.599

Gnomad4 FIN exome

AF:

0.534

Gnomad4 NFE exome

AF:

0.568

Gnomad4 OTH exome

AF:

0.577

GnomAD4 genome

AF:

0.631

AC:

95893

AN:

151980

Hom.:

31776

Cov.:

AF XY:

0.626

AC XY:

46490

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.856

Gnomad4 AMR

AF:

0.476

Gnomad4 ASJ

AF:

0.508

Gnomad4 EAS

AF:

0.560

Gnomad4 SAS

AF:

0.602

Gnomad4 FIN

AF:

0.538

Gnomad4 NFE

AF:

0.559

Gnomad4 OTH

AF:

0.571

Alfa

AF:

0.579

Hom.:

13818

Bravo

AF:

0.633

Asia WGS

AF:

0.621

AC:

2158

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.1

DANN

Benign

0.43

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over