chr13-97985663-CT-C

Position:

• chr13-97985663-CT-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_002271.6(IPO5):​c.364+64del 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 0.54 (21645 hom., cov: 0)
  • Exomes 𝑓: 0.47 (30311 hom.)
  • Failed GnomAD Quality Control
• 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IPO5	NM_002271.6	c.364+64del		intron_variant		ENST00000651721.2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.544 AC: 79192 AN: 145584 Hom.: 21627 Cov.: 0

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.431

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.492

GnomAD3 exomes AF: 0.511 AC: 66601 AN: 130350 Hom.: 7363 AF XY: 0.514 AC XY: 36597 AN XY: 71246

Gnomad AFR exome AF: 0.543

Gnomad AMR exome AF: 0.462

Gnomad ASJ exome AF: 0.497

Gnomad EAS exome AF: 0.386

Gnomad SAS exome AF: 0.498

Gnomad FIN exome AF: 0.536

Gnomad NFE exome AF: 0.537

Gnomad OTH exome AF: 0.503

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.466 AC: 356828 AN: 765850 Hom.: 30311 Cov.: 0 AF XY: 0.467 AC XY: 185961 AN XY: 398000

Gnomad4 AFR exome AF: 0.482

Gnomad4 AMR exome AF: 0.415

Gnomad4 ASJ exome AF: 0.449

Gnomad4 EAS exome AF: 0.366

Gnomad4 SAS exome AF: 0.450

Gnomad4 FIN exome AF: 0.478

Gnomad4 NFE exome AF: 0.476

Gnomad4 OTH exome AF: 0.463

GnomAD4 genome AF: 0.544 AC: 79233 AN: 145638 Hom.: 21645 Cov.: 0 AF XY: 0.539 AC XY: 38106 AN XY: 70640

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.490

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;