Variant rs2306641 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_015024.5(XPO7):c.696C>T(p.Ile232Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,613,512 control chromosomes in the GnomAD database, including 135,034 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 0.36 ( 10189 hom., cov: 32)

Exomes 𝑓: 0.41 ( 124845 hom. )

Consequence

XPO7
NM_015024.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.206

Variant links:

Genes affected

XPO7 (HGNC:14108): (exportin 7) The transport of protein and large RNAs through the nuclear pore complexes (NPC) is an energy-dependent and regulated process. The import of proteins with a nuclear localization signal (NLS) is accomplished by recognition of one or more clusters of basic amino acids by the importin-alpha/beta complex; see MIM 600685 and MIM 602738. The small GTPase RAN (MIM 601179) plays a key role in NLS-dependent protein import. RAN-binding protein-16 is a member of the importin-beta superfamily of nuclear transport receptors.[supplied by OMIM, Jul 2002]

XPO7 links:

XPO7 (HGNC:):

XPO7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BP7

Synonymous conserved (PhyloP=0.206 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XPO7	NM_015024.5 linkuse as main transcript	c.696C>T	p.Ile232Ile	synonymous_variant	7/28	ENST00000252512.14	NP_055839.3	Q9UIA9
XPO7	NM_001100161.2 linkuse as main transcript	c.723C>T	p.Ile241Ile	synonymous_variant	7/28		NP_001093631.1
XPO7	NM_001362802.2 linkuse as main transcript	c.630C>T	p.Ile210Ile	synonymous_variant	6/27		NP_001349731.1
XPO7	NR_156173.2 linkuse as main transcript	n.805C>T		non_coding_transcript_exon_variant	7/29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
XPO7	ENST00000252512.14 linkuse as main transcript	c.696C>T	p.Ile232Ile	synonymous_variant	7/28	1	NM_015024.5	ENSP00000252512.9	Q9UIA9
XPO7	ENST00000518017.1 linkuse as main transcript	n.891C>T		non_coding_transcript_exon_variant	7/7	1
XPO7	ENST00000433566.8 linkuse as main transcript	c.699C>T	p.Ile233Ile	synonymous_variant	7/28	5		ENSP00000410249.3	E7ESC6

Frequencies

GnomAD3 genomes

AF:

0.356

AC:

54005

AN:

151854

Hom.:

10188

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.467

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.393

Gnomad EAS

AF:

0.404

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.458

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.424

Gnomad OTH

AF:

0.365

GnomAD3 exomes

AF:

0.352

AC:

87746

AN:

249124

Hom.:

17124

AF XY:

0.354

AC XY:

47814

AN XY:

135132

show subpopulations

Gnomad AFR exome

AF:

0.260

Gnomad AMR exome

AF:

0.180

Gnomad ASJ exome

AF:

0.388

Gnomad EAS exome

AF:

0.419

Gnomad SAS exome

AF:

0.189

Gnomad FIN exome

AF:

0.447

Gnomad NFE exome

AF:

0.429

Gnomad OTH exome

AF:

0.367

GnomAD4 exome

AF:

0.405

AC:

592505

AN:

1461540

Hom.:

124845

Cov.:

AF XY:

0.400

AC XY:

290760

AN XY:

727060

show subpopulations

Gnomad4 AFR exome

AF:

0.263

Gnomad4 AMR exome

AF:

0.189

Gnomad4 ASJ exome

AF:

0.386

Gnomad4 EAS exome

AF:

0.355

Gnomad4 SAS exome

AF:

0.194

Gnomad4 FIN exome

AF:

0.447

Gnomad4 NFE exome

AF:

0.436

Gnomad4 OTH exome

AF:

0.395

GnomAD4 genome

AF:

0.355

AC:

54024

AN:

151972

Hom.:

10189

Cov.:

AF XY:

0.351

AC XY:

26091

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.261

Gnomad4 AMR

AF:

0.257

Gnomad4 ASJ

AF:

0.393

Gnomad4 EAS

AF:

0.404

Gnomad4 SAS

AF:

0.189

Gnomad4 FIN

AF:

0.458

Gnomad4 NFE

AF:

0.424

Gnomad4 OTH

AF:

0.368

Alfa

AF:

0.406

Hom.:

26102

Bravo

AF:

0.341

Asia WGS

AF:

0.328

AC:

1141

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

8.1

DANN

Benign

0.68

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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