6-116732074-TTATATATATATATATATATATATATATATATATATATATATA-TTATATATATATATATATATATATATA

Variant summary

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

The NM_001366306.2(KPNA5):​c.1433-29_1433-14del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 67,642 control chromosomes in the GnomAD database, including 53 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 0.022 ( 47 hom., cov: 0)
Exomes 𝑓: 0.028 ( 6 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0665 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KPNA5NM_001366306.2 linkuse as main transcriptc.1433-29_1433-14del intron_variant ENST00000368564.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KPNA5ENST00000368564.7 linkuse as main transcriptc.1433-29_1433-14del intron_variant 1 NM_001366306.2 P4

Frequencies

GnomAD3 genomes
AF:
0.0217
AC:
1020
AN:
46908
Hom.:
47
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0436
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00857
Gnomad ASJ
AF:
0.00140
Gnomad EAS
AF:
0.0104
Gnomad SAS
AF:
0.00483
Gnomad FIN
AF:
0.0228
Gnomad MID
AF:
0.0179
Gnomad NFE
AF:
0.0133
Gnomad OTH
AF:
0.0176
GnomAD4 exome
AF:
0.0284
AC:
588
AN:
20734
Hom.:
6
AF XY:
0.0274
AC XY:
322
AN XY:
11756
show subpopulations
Gnomad4 AFR exome
AF:
0.0242
Gnomad4 AMR exome
AF:
0.0836
Gnomad4 ASJ exome
AF:
0.0227
Gnomad4 EAS exome
AF:
0.00667
Gnomad4 SAS exome
AF:
0.00859
Gnomad4 FIN exome
AF:
0.0291
Gnomad4 NFE exome
AF:
0.0300
Gnomad4 OTH exome
AF:
0.0348
GnomAD4 genome
AF:
0.0218
AC:
1021
AN:
46908
Hom.:
47
Cov.:
0
AF XY:
0.0217
AC XY:
468
AN XY:
21548
show subpopulations
Gnomad4 AFR
AF:
0.0436
Gnomad4 AMR
AF:
0.00857
Gnomad4 ASJ
AF:
0.00140
Gnomad4 EAS
AF:
0.0105
Gnomad4 SAS
AF:
0.00483
Gnomad4 FIN
AF:
0.0228
Gnomad4 NFE
AF:
0.0133
Gnomad4 OTH
AF:
0.0175

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.

Other links and lift over

dbSNP: rs2243369; hg19: chr6-117053237; API