13-98006356-ATTTTTTTTTTTTTTTTTTTTTTTT-ATTTTTTTTTTTT

Variant names:

• chr13-98006356-ATTTTTTTTTTTT-A
• rs568589408
• NM_002271.6:c.1716+33_1716+44delTTTTTTTTTTTT

Variant summary

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

The NM_002271.6(IPO5):​c.1716+33_1716+44delTTTTTTTTTTTT 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 0.035 (55 hom., cov: 0)
  • Exomes 𝑓: 0.034 (492 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+33_1716+44delTTTTTTTTTTTT		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+20delTTTTTTTTTTTT		intron_variant	Intron 17 of 28		NM_002271.6	ENSP00000499125.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2186 AN: 62666 Hom.: 55 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0543

Gnomad EAS AF: 0.0861

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.00586

Gnomad MID AF: 0.0326

Gnomad NFE AF: 0.00884

Gnomad OTH AF: 0.0392

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0336 AC: 16388 AN: 487952 Hom.: 492 AF XY: 0.0337 AC XY: 8703 AN XY: 257954

Gnomad4 AFR exome AF: 0.0661

Gnomad4 AMR exome AF: 0.0986

Gnomad4 ASJ exome AF: 0.0462

Gnomad4 EAS exome AF: 0.0579

Gnomad4 SAS exome AF: 0.0366

Gnomad4 FIN exome AF: 0.0243

Gnomad4 NFE exome AF: 0.0281

Gnomad4 OTH exome AF: 0.0378

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0349 AC: 2189 AN: 62678 Hom.: 55 Cov.: 0 AF XY: 0.0372 AC XY: 1045 AN XY: 28086

Gnomad4 AFR AF: 0.0749

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0543

Gnomad4 EAS AF: 0.0866

Gnomad4 SAS AF: 0.0292

Gnomad4 FIN AF: 0.00586

Gnomad4 NFE AF: 0.00884

Gnomad4 OTH AF: 0.0400

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;