GeneBe

rs9297145

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_017012211.2(KPNA7):​c.1546-15178G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,014 control chromosomes in the GnomAD database, including 35,431 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.67 ( 35431 hom., cov: 32)

Consequence

KPNA7
XM_017012211.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.950
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KPNA7XM_017012211.2 linkuse as main transcriptc.1546-15178G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.672
AC:
102000
AN:
151896
Hom.:
35411
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.486
Gnomad AMI
AF:
0.765
Gnomad AMR
AF:
0.734
Gnomad ASJ
AF:
0.705
Gnomad EAS
AF:
0.901
Gnomad SAS
AF:
0.620
Gnomad FIN
AF:
0.791
Gnomad MID
AF:
0.741
Gnomad NFE
AF:
0.734
Gnomad OTH
AF:
0.660
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.671
AC:
102067
AN:
152014
Hom.:
35431
Cov.:
32
AF XY:
0.675
AC XY:
50181
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.487
Gnomad4 AMR
AF:
0.734
Gnomad4 ASJ
AF:
0.705
Gnomad4 EAS
AF:
0.901
Gnomad4 SAS
AF:
0.622
Gnomad4 FIN
AF:
0.791
Gnomad4 NFE
AF:
0.734
Gnomad4 OTH
AF:
0.657
Alfa
AF:
0.724
Hom.:
81432
Bravo
AF:
0.662
Asia WGS
AF:
0.708
AC:
2465
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
3.4
DANN
Benign
0.83

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: rs9297145; hg19: chr7-98759117; API