chr13-97985663-C-CTT

Position:

• chr13-97985663-C-CTT

Variant summary

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

The NM_002271.6(IPO5):​c.364+63_364+64dup 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 0.000021 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00051 (0 hom.)
• Consequence: IPO5 NM_002271.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

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/exons	MANE	UniProt
IPO5	NM_002271.6	c.364+63_364+64dup		intron_variant		ENST00000651721.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IPO5	ENST00000651721.2	c.364+63_364+64dup		intron_variant			NM_002271.6	P1

Frequencies

GnomAD3 genomes AF: 0.0000206 AC: 3 AN: 145834 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000757

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000445 AC: 58 AN: 130350 Hom.: 0 AF XY: 0.000379 AC XY: 27 AN XY: 71246

Gnomad AFR exome AF: 0.000117

Gnomad AMR exome AF: 0.00103

Gnomad ASJ exome AF: 0.000385

Gnomad EAS exome AF: 0.00135

Gnomad SAS exome AF: 0.000572

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000295

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000509 AC: 399 AN: 784358 Hom.: 0 Cov.: 0 AF XY: 0.000480 AC XY: 196 AN XY: 407932

Gnomad4 AFR exome AF: 0.000354

Gnomad4 AMR exome AF: 0.000756

Gnomad4 ASJ exome AF: 0.000429

Gnomad4 EAS exome AF: 0.000598

Gnomad4 SAS exome AF: 0.000704

Gnomad4 FIN exome AF: 0.0000225

Gnomad4 NFE exome AF: 0.000519

Gnomad4 OTH exome AF: 0.000496

GnomAD4 genome AF: 0.0000206 AC: 3 AN: 145834 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 70708

Gnomad4 AFR AF: 0.0000757

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

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: rs11366582; hg19: chr13-98637917;