rs4041421

Variant summary

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

The ENST00000337273.10(TNPO1):​c.15+14890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,764 control chromosomes in the GnomAD database, including 18,270 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 0.47 ( 18270 hom., cov: 32)

Consequence

TNPO1
ENST00000337273.10 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65
Variant links:
Genes affected
TNPO1 (HGNC:6401): (transportin 1) This gene encodes the beta subunit of the karyopherin receptor complex which interacts with nuclear localization signals to target nuclear proteins to the nucleus. The karyopherin receptor complex is a heterodimer of an alpha subunit which recognizes the nuclear localization signal and a beta subunit which docks the complex at nucleoporins. Alternate splicing of this gene results in several transcript variants encoding different proteins. [provided by RefSeq, Jun 2018]

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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TNPO1NM_002270.4 linkuse as main transcriptc.15+14890C>T intron_variant ENST00000337273.10 NP_002261.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TNPO1ENST00000337273.10 linkuse as main transcriptc.15+14890C>T intron_variant 1 NM_002270.4 ENSP00000336712 Q92973-1

Frequencies

GnomAD3 genomes
AF:
0.474
AC:
71868
AN:
151648
Hom.:
18255
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.273
Gnomad AMI
AF:
0.582
Gnomad AMR
AF:
0.607
Gnomad ASJ
AF:
0.567
Gnomad EAS
AF:
0.404
Gnomad SAS
AF:
0.524
Gnomad FIN
AF:
0.584
Gnomad MID
AF:
0.566
Gnomad NFE
AF:
0.544
Gnomad OTH
AF:
0.507
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.474
AC:
71907
AN:
151764
Hom.:
18270
Cov.:
32
AF XY:
0.478
AC XY:
35409
AN XY:
74130
show subpopulations
Gnomad4 AFR
AF:
0.273
Gnomad4 AMR
AF:
0.607
Gnomad4 ASJ
AF:
0.567
Gnomad4 EAS
AF:
0.404
Gnomad4 SAS
AF:
0.525
Gnomad4 FIN
AF:
0.584
Gnomad4 NFE
AF:
0.544
Gnomad4 OTH
AF:
0.510
Alfa
AF:
0.488
Hom.:
2553
Bravo
AF:
0.466
Asia WGS
AF:
0.473
AC:
1619
AN:
3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.51
DANN
Benign
0.65

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: rs4041421; hg19: chr5-72127469; API