rs7843479

Variant names:

• chr8-21963302-C-A
• rs7843479
• NM_015024.5:c.19-3555C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-21963302-C-A
• chr8-21963302-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015024.5(XPO7):​c.19-3555C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,994 control chromosomes in the GnomAD database, including 10,484 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 (10484 hom., cov: 32)
• Consequence: XPO7 NM_015024.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 26 publications found

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 Gene-Disease associations (from GenCC):

• prostate cancer

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015024.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XPO7	NM_015024.5	MANE Select	c.19-3555C>A		intron	N/A	NP_055839.3
	XPO7	NM_001100161.2		c.19-3555C>A		intron	N/A	NP_001093631.1
	XPO7	NM_001362802.2		c.19-3555C>A		intron	N/A	NP_001349731.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XPO7	ENST00000252512.14	TSL:1 MANE Select	c.19-3555C>A		intron	N/A	ENSP00000252512.9	Q9UIA9
	XPO7	ENST00000518017.1	TSL:1	n.214-3555C>A		intron	N/A
	XPO7	ENST00000879832.1		c.19-3555C>A		intron	N/A	ENSP00000549891.1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55064 AN: 151874 Hom.: 10478 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.371

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.362 AC: 55090 AN: 151994 Hom.: 10484 Cov.: 32 AF XY: 0.358 AC XY: 26609 AN XY: 74292

African (AFR) AF: 0.287 AC: 11887 AN: 41472

American (AMR) AF: 0.259 AC: 3948 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3470

East Asian (EAS) AF: 0.403 AC: 2081 AN: 5170

South Asian (SAS) AF: 0.189 AC: 909 AN: 4816

European-Finnish (FIN) AF: 0.456 AC: 4807 AN: 10542

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28760 AN: 67938

Other (OTH) AF: 0.374 AC: 790 AN: 2114

Alfa AF: 0.398 Hom.: 43205

Bravo AF: 0.349

Asia WGS AF: 0.330 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.68
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7843479; hg19: chr8-21820813;