13-98006356-ATTTTTTTTTTTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTTTTTTT

Variant names:

• chr13-98006356-A-AT
• rs568589408
• NM_002271.6:c.1716+44dupT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_002271.6(IPO5):​c.1716+44dupT 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 (628 hom., cov: 0)
  • Exomes 𝑓: 0.0077 (54 hom.)
  • Failed GnomAD Quality Control
• Consequence: IPO5 NM_002271.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0351 (2206/62832) while in subpopulation NFE AF= 0.0403 (1498/37126). AF 95% confidence interval is 0.0386. There are 628 homozygotes in gnomad4. There are 945 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 628 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IPO5	NM_002271.6	c.1716+44dupT		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+8_1716+9insT		intron_variant	Intron 17 of 28		NM_002271.6	ENSP00000499125.1

Frequencies

GnomAD3 genomes AF: 0.0351 AC: 2206 AN: 62822 Hom.: 628 Cov.: 0

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.0607

Gnomad AMR AF: 0.0269

Gnomad ASJ AF: 0.0489

Gnomad EAS AF: 0.0118

Gnomad SAS AF: 0.0127

Gnomad FIN AF: 0.00528

Gnomad MID AF: 0.0652

Gnomad NFE AF: 0.0403

Gnomad OTH AF: 0.0329

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00766 AC: 3772 AN: 492586 Hom.: 54 Cov.: 0 AF XY: 0.00804 AC XY: 2093 AN XY: 260404

Gnomad4 AFR exome AF: 0.00542

Gnomad4 AMR exome AF: 0.00705

Gnomad4 ASJ exome AF: 0.00861

Gnomad4 EAS exome AF: 0.00186

Gnomad4 SAS exome AF: 0.0142

Gnomad4 FIN exome AF: 0.00862

Gnomad4 NFE exome AF: 0.00695

Gnomad4 OTH exome AF: 0.00903

GnomAD4 genome AF: 0.0351 AC: 2206 AN: 62832 Hom.: 628 Cov.: 0 AF XY: 0.0336 AC XY: 945 AN XY: 28144

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.0268

Gnomad4 ASJ AF: 0.0489

Gnomad4 EAS AF: 0.0119

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.00528

Gnomad4 NFE AF: 0.0403

Gnomad4 OTH AF: 0.0325

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;