rs7843479

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XPO7	NM_015024.5	c.19-3555C>A		intron_variant		ENST00000252512.14	NP_055839.3
XPO7	NM_001100161.2	c.19-3555C>A		intron_variant			NP_001093631.1
XPO7	NM_001362802.2	c.19-3555C>A		intron_variant			NP_001349731.1
XPO7	NR_156173.2	n.128-3555C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XPO7	ENST00000252512.14	c.19-3555C>A		intron_variant		1	NM_015024.5	ENSP00000252512.9

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

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.374

Alfa AF: 0.403 Hom.: 19435

Bravo AF: 0.349

Asia WGS AF: 0.330 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.68

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

Other links and lift over

dbSNP: rs7843479; hg19: chr8-21820813;