Variant 8-21970322-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015024.5(XPO7):c.426+12A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 1,609,164 control chromosomes in the GnomAD database, including 138,269 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 ( 10514 hom., cov: 31)

Exomes 𝑓: 0.41 ( 127755 hom. )

Consequence

XPO7
NM_015024.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
XPO7	NM_015024.5 linkuse as main transcript	c.426+12A>G	intron_variant	ENST00000252512.14	NP_055839.3
XPO7	NM_001100161.2 linkuse as main transcript	c.426+12A>G	intron_variant		NP_001093631.1
XPO7	NM_001362802.2 linkuse as main transcript	c.426+12A>G	intron_variant		NP_001349731.1
XPO7	NR_156173.2 linkuse as main transcript	n.535+12A>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
XPO7	ENST00000252512.14 linkuse as main transcript	c.426+12A>G	intron_variant	1	NM_015024.5	ENSP00000252512	P1
XPO7	ENST00000518017.1 linkuse as main transcript	n.621+12A>G	intron_variant, non_coding_transcript_variant	1
XPO7	ENST00000433566.8 linkuse as main transcript	c.429+12A>G	intron_variant	5		ENSP00000410249
XPO7	ENST00000521303.5 linkuse as main transcript	c.440+12A>G	intron_variant	5		ENSP00000429290

Frequencies

GnomAD3 genomes

AF:

0.363

AC:

55096

AN:

151728

Hom.:

10517

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.468

Gnomad AMR

AF:

0.289

Gnomad ASJ

AF:

0.396

Gnomad EAS

AF:

0.442

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.456

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.426

Gnomad OTH

AF:

0.373

GnomAD3 exomes

AF:

0.369

AC:

90205

AN:

244348

Hom.:

17806

AF XY:

0.368

AC XY:

48851

AN XY:

132620

show subpopulations

Gnomad AFR exome

AF:

0.268

Gnomad AMR exome

AF:

0.256

Gnomad ASJ exome

AF:

0.395

Gnomad EAS exome

AF:

0.452

Gnomad SAS exome

AF:

0.195

Gnomad FIN exome

AF:

0.448

Gnomad NFE exome

AF:

0.433

Gnomad OTH exome

AF:

0.377

GnomAD4 exome

AF:

0.412

AC:

600855

AN:

1457318

Hom.:

127755

Cov.:

AF XY:

0.407

AC XY:

294601

AN XY:

724718

show subpopulations

Gnomad4 AFR exome

AF:

0.270

Gnomad4 AMR exome

AF:

0.259

Gnomad4 ASJ exome

AF:

0.390

Gnomad4 EAS exome

AF:

0.423

Gnomad4 SAS exome

AF:

0.197

Gnomad4 FIN exome

AF:

0.447

Gnomad4 NFE exome

AF:

0.439

Gnomad4 OTH exome

AF:

0.401

GnomAD4 genome

AF:

0.363

AC:

55118

AN:

151846

Hom.:

10514

Cov.:

AF XY:

0.359

AC XY:

26613

AN XY:

74194

show subpopulations

Gnomad4 AFR

AF:

0.268

Gnomad4 AMR

AF:

0.289

Gnomad4 ASJ

AF:

0.396

Gnomad4 EAS

AF:

0.441

Gnomad4 SAS

AF:

0.189

Gnomad4 FIN

AF:

0.456

Gnomad4 NFE

AF:

0.426

Gnomad4 OTH

AF:

0.375

Alfa

AF:

0.383

Hom.:

3012

Bravo

AF:

0.352

Asia WGS

AF:

0.348

AC:

1211

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.33

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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