Variant chr6-116732074-TTATATATATATATATATATATATATA-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001366306.2(KPNA5):c.1433-39_1433-14del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 67,720 control chromosomes in the GnomAD database, including 278 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 0.052 ( 154 hom., cov: 0)

Exomes 𝑓: 0.056 ( 124 hom. )

Consequence

KPNA5
NM_001366306.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Variant links:

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]

KPNA5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KPNA5	NM_001366306.2 linkuse as main transcript	c.1433-39_1433-14del		intron_variant		ENST00000368564.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KPNA5	ENST00000368564.7 linkuse as main transcript	c.1433-39_1433-14del		intron_variant		1	NM_001366306.2	P4

Frequencies

GnomAD3 genomes

AF:

0.0518

AC:

2430

AN:

46920

Hom.:

155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0109

Gnomad ASJ

AF:

0.0414

Gnomad EAS

AF:

0.00553

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0893

Gnomad NFE

AF:

0.00311

Gnomad OTH

AF:

0.0463

GnomAD4 exome

AF:

0.0563

AC:

1172

AN:

20800

Hom.:

124

AF XY:

0.0605

AC XY:

714

AN XY:

11796

show subpopulations

Gnomad4 AFR exome

AF:

0.247

Gnomad4 AMR exome

AF:

0.0333

Gnomad4 ASJ exome

AF:

0.150

Gnomad4 EAS exome

AF:

0.0154

Gnomad4 SAS exome

AF:

0.301

Gnomad4 FIN exome

AF:

0.00111

Gnomad4 NFE exome

AF:

0.0135

Gnomad4 OTH exome

AF:

0.108

GnomAD4 genome

AF:

0.0517

AC:

2427

AN:

46920

Hom.:

154

Cov.:

AF XY:

0.0562

AC XY:

1212

AN XY:

21550

show subpopulations

Gnomad4 AFR

AF:

0.134

Gnomad4 AMR

AF:

0.0109

Gnomad4 ASJ

AF:

0.0414

Gnomad4 EAS

AF:

0.00490

Gnomad4 SAS

AF:

0.179

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00311

Gnomad4 OTH

AF:

0.0446

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over