13-98006356-ATTTTTTTTTTTTTTTTTTTTTTTT-ATTTTTTTTTTTTTT

Variant names:

• chr13-98006356-ATTTTTTTTTT-A
• rs568589408
• NM_002271.6:c.1716+35_1716+44delTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_002271.6(IPO5):​c.1716+35_1716+44delTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.25 (463 hom., cov: 0)
  • Exomes 𝑓: 0.12 (4550 hom.)
  • Failed GnomAD Quality Control
• Consequence: IPO5 NM_002271.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

IPO5 (HGNC:6402): (importin 5) Nucleocytoplasmic transport, a signal- and energy-dependent process, takes place through nuclear pore complexes embedded in the nuclear envelope. The import of proteins containing a nuclear localization signal (NLS) requires the NLS import receptor, a heterodimer of importin alpha and beta subunits also known as karyopherins. Importin alpha binds the NLS-containing cargo in the cytoplasm and importin beta docks the complex at the cytoplasmic side of the nuclear pore complex. In the presence of nucleoside triphosphates and the small GTP binding protein Ran, the complex moves into the nuclear pore complex and the importin subunits dissociate. Importin alpha enters the nucleoplasm with its passenger protein and importin beta remains at the pore. Interactions between importin beta and the FG repeats of nucleoporins are essential in translocation through the pore complex. The protein encoded by this gene is a member of the importin beta family. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IPO5	NM_002271.6	c.1716+35_1716+44delTTTTTTTTTT		intron_variant	Intron 17 of 28	ENST00000651721.2	NP_002262.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IPO5	ENST00000651721.2	c.1716+9_1716+18delTTTTTTTTTT		intron_variant	Intron 17 of 28		NM_002271.6	ENSP00000499125.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 15076 AN: 59862 Hom.: 466 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.211

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.242

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.123 AC: 59554 AN: 483726 Hom.: 4550 AF XY: 0.125 AC XY: 31995 AN XY: 255434

Gnomad4 AFR exome AF: 0.0827

Gnomad4 AMR exome AF: 0.0916

Gnomad4 ASJ exome AF: 0.109

Gnomad4 EAS exome AF: 0.00603

Gnomad4 SAS exome AF: 0.121

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.134

Gnomad4 OTH exome AF: 0.127

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.252 AC: 15066 AN: 59874 Hom.: 463 Cov.: 0 AF XY: 0.240 AC XY: 6481 AN XY: 26982

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.239

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs568589408; hg19: chr13-98658610;