rs17616085

Positions:

• chr8-21999756-G-A
• chr8-21999756-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015024.5(XPO7):​c.2782+82G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 1,558,982 control chromosomes in the GnomAD database, including 131,481 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 (10265 hom., cov: 32)
  • Exomes 𝑓: 0.41 (121216 hom.)
• Consequence: XPO7 NM_015024.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) 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.2782+82G>A		intron_variant		ENST00000252512.14	NP_055839.3
XPO7	NM_001100161.2	c.2809+82G>A		intron_variant			NP_001093631.1
XPO7	NM_001362802.2	c.2716+82G>A		intron_variant			NP_001349731.1
XPO7	NR_156173.2	n.3002+82G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XPO7	ENST00000252512.14	c.2782+82G>A		intron_variant		1	NM_015024.5	ENSP00000252512	P1
XPO7	ENST00000433566.8	c.2785+82G>A		intron_variant		5		ENSP00000410249

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54487 AN: 151942 Hom.: 10268 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.369

GnomAD4 exome AF: 0.409 AC: 575193 AN: 1406922 Hom.: 121216 AF XY: 0.403 AC XY: 280949 AN XY: 696928

Gnomad4 AFR exome AF: 0.263

Gnomad4 AMR exome AF: 0.256

Gnomad4 ASJ exome AF: 0.384

Gnomad4 EAS exome AF: 0.418

Gnomad4 SAS exome AF: 0.194

Gnomad4 FIN exome AF: 0.445

Gnomad4 NFE exome AF: 0.434

Gnomad4 OTH exome AF: 0.397

GnomAD4 genome AF: 0.358 AC: 54510 AN: 152060 Hom.: 10265 Cov.: 32 AF XY: 0.355 AC XY: 26360 AN XY: 74316

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.371

Alfa AF: 0.377 Hom.: 1874

Bravo AF: 0.347

Asia WGS AF: 0.343 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.74
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs17616085; hg19: chr8-21857267; COSMIC: COSV53012464; COSMIC: COSV53012464;