GeneBe

rs2243369

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001366306.2(KPNA5):​c.1433-55_1433-14delTATATATATATATATATATATATATATATATATATATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000812 in 67,758 control chromosomes in the GnomAD database, including 10 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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 0.000085 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0024 ( 10 hom. )

Consequence

KPNA5
NM_001366306.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

3 publications found
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

new If you want to explore the variant's impact on the transcript NM_001366306.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2
High Homozygotes in GnomAdExome4 at 10 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366306.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KPNA5
NM_001366306.2
MANE Select
c.1433-55_1433-14delTATATATATATATATATATATATATATATATATATATATATA
intron
N/ANP_001353235.1O15131
KPNA5
NM_001366304.1
c.1493-55_1493-14delTATATATATATATATATATATATATATATATATATATATATA
intron
N/ANP_001353233.1A0A8V8TMV2
KPNA5
NM_001366305.2
c.1493-55_1493-14delTATATATATATATATATATATATATATATATATATATATATA
intron
N/ANP_001353234.1A0A8V8TMV2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KPNA5
ENST00000368564.7
TSL:1 MANE Select
c.1433-61_1433-20delTATATATATATATATATATATATATATATATATATATATATA
intron
N/AENSP00000357552.1O15131
KPNA5
ENST00000356348.6
TSL:1
c.1433-61_1433-20delTATATATATATATATATATATATATATATATATATATATATA
intron
N/AENSP00000348704.1O15131
KPNA5
ENST00000937498.1
c.1508-61_1508-20delTATATATATATATATATATATATATATATATATATATATATA
intron
N/AENSP00000607557.1

Frequencies

GnomAD3 genomes
AF:
0.0000853
AC:
4
AN:
46916
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000186
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00245
AC:
51
AN:
20842
Hom.:
10
AF XY:
0.00254
AC XY:
30
AN XY:
11818
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
958
American (AMR)
AF:
0.00
AC:
0
AN:
722
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
976
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1050
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1632
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
3588
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
64
European-Non Finnish (NFE)
AF:
0.00451
AC:
49
AN:
10870
Other (OTH)
AF:
0.00204
AC:
2
AN:
982
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.799
Heterozygous variant carriers
0
2
4
5
7
9
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0000853
AC:
4
AN:
46916
Hom.:
0
Cov.:
0
AF XY:
0.0000464
AC XY:
1
AN XY:
21550
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
14518
American (AMR)
AF:
0.00
AC:
0
AN:
4666
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
1426
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1446
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1448
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
1054
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
56
European-Non Finnish (NFE)
AF:
0.000186
AC:
4
AN:
21536
Other (OTH)
AF:
0.00
AC:
0
AN:
626
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.650
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.0
BranchPoint Hunter
2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

Other links and lift over

dbSNP: rs2243369;
hg19: chr6-117053237;
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