6-116732074-TTATATATATATATATATATATATATATATATATATATATATA-TTATATATATATATATATATATATATATATATATATATATATATATA

Position:

• chr6-116732074-TTATATATATATATATATATATATATATATATATATATATATA-TTATATATATATATATATATATATATATATATATATATATATATATA

Variant summary

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

The NM_001366306.2(KPNA5):​c.1433-17_1433-14dupTATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 67,284 control chromosomes in the GnomAD database, including 34 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. There are indicators that this mutation may affect the branch point..

• Frequency:
  • Genomes: 𝑓 0.017 (34 hom., cov: 12)
  • Exomes 𝑓: 0.0010 (0 hom.)
• Consequence: KPNA5 NM_001366306.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

KPNA5 (HGNC:6398): (karyopherin subunit alpha 5) The transport of molecules between the nucleus and the cytoplasm in eukaryotic cells is mediated by the nuclear pore complex (NPC) which consists of 60-100 proteins and is probably 120 million daltons in molecular size. Small molecules (up to 70 kD) can pass through the nuclear pore by nonselective diffusion; larger molecules are transported by an active process. Most nuclear proteins contain short basic amino acid sequences known as nuclear localization signals (NLSs). KPNA5 protein belongs to the importin alpha protein family and is thought to be involved in NLS-dependent protein import into the nucleus. [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 = 0.0172 (799/46492) while in subpopulation NFE AF= 0.023 (491/21336). AF 95% confidence interval is 0.0213. There are 34 homozygotes in gnomad4. There are 370 alleles in male gnomad4 subpopulation. Median coverage is 12. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 34 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KPNA5	NM_001366306.2	c.1433-17_1433-14dupTATA		intron_variant		ENST00000368564.7	NP_001353235.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KPNA5	ENST00000368564.7	c.1433-17_1433-14dupTATA		intron_variant		1	NM_001366306.2	ENSP00000357552.1

Frequencies

GnomAD3 genomes AF: 0.0172 AC: 799 AN: 46492 Hom.: 34 Cov.: 12

Gnomad AFR AF: 0.00831

Gnomad AMI AF: 0.0145

Gnomad AMR AF: 0.0183

Gnomad ASJ AF: 0.0388

Gnomad EAS AF: 0.0134

Gnomad SAS AF: 0.00772

Gnomad FIN AF: 0.00381

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0230

Gnomad OTH AF: 0.0227

GnomAD4 exome AF: 0.00101 AC: 21 AN: 20792 Hom.: 0 AF XY: 0.00102 AC XY: 12 AN XY: 11782

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00139

Gnomad4 ASJ exome AF: 0.00307

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00140

Gnomad4 NFE exome AF: 0.00101

Gnomad4 OTH exome AF: 0.00102

GnomAD4 genome AF: 0.0172 AC: 799 AN: 46492 Hom.: 34 Cov.: 12 AF XY: 0.0173 AC XY: 370 AN XY: 21366

Gnomad4 AFR AF: 0.00830

Gnomad4 AMR AF: 0.0183

Gnomad4 ASJ AF: 0.0388

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.00702

Gnomad4 FIN AF: 0.00381

Gnomad4 NFE AF: 0.0230

Gnomad4 OTH AF: 0.0226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BranchPoint Hunter		2.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243369; hg19: chr6-117053237;