Variant rs4910052 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006391.3(IPO7):c.2055T>C(p.Asp685=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0662 in 1,610,730 control chromosomes in the GnomAD database, including 4,074 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 0.048 ( 243 hom., cov: 31)

Exomes 𝑓: 0.068 ( 3831 hom. )

Consequence

IPO7
NM_006391.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.84

Variant links:

Genes affected

IPO7 (HGNC:9852): (importin 7) The importin-alpha/beta complex and the GTPase Ran mediate nuclear import of proteins with a classical nuclear localization signal. The protein encoded by this gene is a member of a class of approximately 20 potential Ran targets that share a sequence motif related to the Ran-binding site of importin-beta. Similar to importin-beta, this protein prevents the activation of Ran's GTPase by RanGAP1 and inhibits nucleotide exchange on RanGTP, and also binds directly to nuclear pore complexes where it competes for binding sites with importin-beta and transportin. This protein has a Ran-dependent transport cycle and it can cross the nuclear envelope rapidly and in both directions. At least four importin beta-like transport receptors, namely importin beta itself, transportin, RanBP5 and RanBP7, directly bind and import ribosomal proteins. [provided by RefSeq, Jul 2008]

IPO7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP7

Synonymous conserved (PhyloP=1.84 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IPO7	NM_006391.3 linkuse as main transcript	c.2055T>C	p.Asp685=	synonymous_variant	18/25	ENST00000379719.8	NP_006382.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IPO7	ENST00000379719.8 linkuse as main transcript	c.2055T>C	p.Asp685=	synonymous_variant	18/25	1	NM_006391.3	ENSP00000369042	P1

Frequencies

GnomAD3 genomes

AF:

0.0478

AC:

7280

AN:

152150

Hom.:

243

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0130

Gnomad AMI

AF:

0.0934

Gnomad AMR

AF:

0.0353

Gnomad ASJ

AF:

0.0654

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0783

Gnomad FIN

AF:

0.0531

Gnomad MID

AF:

0.0255

Gnomad NFE

AF:

0.0713

Gnomad OTH

AF:

0.0421

GnomAD3 exomes

AF:

0.0546

AC:

13681

AN:

250658

Hom.:

519

AF XY:

0.0587

AC XY:

7953

AN XY:

135530

show subpopulations

Gnomad AFR exome

AF:

0.0116

Gnomad AMR exome

AF:

0.0229

Gnomad ASJ exome

AF:

0.0646

Gnomad EAS exome

AF:

0.000326

Gnomad SAS exome

AF:

0.0832

Gnomad FIN exome

AF:

0.0530

Gnomad NFE exome

AF:

0.0706

Gnomad OTH exome

AF:

0.0598

GnomAD4 exome

AF:

0.0681

AC:

99286

AN:

1458462

Hom.:

3831

Cov.:

AF XY:

0.0685

AC XY:

49737

AN XY:

725634

show subpopulations

Gnomad4 AFR exome

AF:

0.0103

Gnomad4 AMR exome

AF:

0.0241

Gnomad4 ASJ exome

AF:

0.0643

Gnomad4 EAS exome

AF:

0.000202

Gnomad4 SAS exome

AF:

0.0828

Gnomad4 FIN exome

AF:

0.0528

Gnomad4 NFE exome

AF:

0.0742

Gnomad4 OTH exome

AF:

0.0596

GnomAD4 genome

AF:

0.0478

AC:

7277

AN:

152268

Hom.:

243

Cov.:

AF XY:

0.0471

AC XY:

3508

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0129

Gnomad4 AMR

AF:

0.0352

Gnomad4 ASJ

AF:

0.0654

Gnomad4 EAS

AF:

0.000771

Gnomad4 SAS

AF:

0.0778

Gnomad4 FIN

AF:

0.0531

Gnomad4 NFE

AF:

0.0713

Gnomad4 OTH

AF:

0.0421

Alfa

AF:

0.0603

Hom.:

215

Bravo

AF:

0.0432

Asia WGS

AF:

0.0230

AC:

AN:

3478

EpiCase

AF:

0.0687

EpiControl

AF:

0.0615

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

7.7

DANN

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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