Variant chr5-72887228-CCTAAGTCCAGTTTGAATTATGTAAGTTGGCTTCTTACTACTATTAGGTACTAATAAGGCTAGGCTACTTTAAGG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000337273.10(TNPO1):c.1303+7_1303+80delCTAAGTCCAGTTTGAATTATGTAAGTTGGCTTCTTACTACTATTAGGTACTAATAAGGCTAGGCTACTTTAAGG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 1,587,068 control chromosomes in the GnomAD database, including 18,725 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1701 hom., cov: 30)

Exomes 𝑓: 0.14 ( 17024 hom. )

Consequence

TNPO1
ENST00000337273.10 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.52

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]

TNPO1 links:

TNPO1 (HGNC:):

TNPO1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-72887228-CCTAAGTCCAGTTTGAATTATGTAAGTTGGCTTCTTACTACTATTAGGTACTAATAAGGCTAGGCTACTTTAAGG-C is Benign according to our data. Variant chr5-72887228-CCTAAGTCCAGTTTGAATTATGTAAGTTGGCTTCTTACTACTATTAGGTACTAATAAGGCTAGGCTACTTTAAGG-C is described in ClinVar as [Benign]. Clinvar id is 771379.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNPO1	NM_002270.4 linkuse as main transcript	c.1303+7_1303+80delCTAAGTCCAGTTTGAATTATGTAAGTTGGCTTCTTACTACTATTAGGTACTAATAAGGCTAGGCTACTTTAAGG		splice_region_variant, intron_variant		ENST00000337273.10	NP_002261.3	Q92973-1A0A024RAM0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNPO1	ENST00000337273.10 linkuse as main transcript	c.1303+7_1303+80delCTAAGTCCAGTTTGAATTATGTAAGTTGGCTTCTTACTACTATTAGGTACTAATAAGGCTAGGCTACTTTAAGG		splice_region_variant, intron_variant		1	NM_002270.4	ENSP00000336712.5		Q92973-1

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20598

AN:

150208

Hom.:

1701

Cov.:

show subpopulations

Gnomad AFR

AF:

0.120

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.0981

Gnomad ASJ

AF:

0.0619

Gnomad EAS

AF:

0.339

Gnomad SAS

AF:

0.0560

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.145

Gnomad OTH

AF:

0.111

GnomAD3 exomes

AF:

0.134

AC:

33139

AN:

247172

Hom.:

2892

AF XY:

0.130

AC XY:

17397

AN XY:

133712

show subpopulations

Gnomad AFR exome

AF:

0.117

Gnomad AMR exome

AF:

0.0928

Gnomad ASJ exome

AF:

0.0705

Gnomad EAS exome

AF:

0.352

Gnomad SAS exome

AF:

0.0483

Gnomad FIN exome

AF:

0.184

Gnomad NFE exome

AF:

0.134

Gnomad OTH exome

AF:

0.131

GnomAD4 exome

AF:

0.137

AC:

197291

AN:

1436742

Hom.:

17024

AF XY:

0.135

AC XY:

96270

AN XY:

715108

show subpopulations

Gnomad4 AFR exome

AF:

0.115

Gnomad4 AMR exome

AF:

0.0988

Gnomad4 ASJ exome

AF:

0.0711

Gnomad4 EAS exome

AF:

0.361

Gnomad4 SAS exome

AF:

0.0515

Gnomad4 FIN exome

AF:

0.196

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.134

GnomAD4 genome

AF:

0.137

AC:

20600

AN:

150326

Hom.:

1701

Cov.:

AF XY:

0.138

AC XY:

10097

AN XY:

73408

show subpopulations

Gnomad4 AFR

AF:

0.120

Gnomad4 AMR

AF:

0.0980

Gnomad4 ASJ

AF:

0.0619

Gnomad4 EAS

AF:

0.340

Gnomad4 SAS

AF:

0.0559

Gnomad4 FIN

AF:

0.185

Gnomad4 NFE

AF:

0.145

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.139

Hom.:

151

Asia WGS

AF:

0.173

AC:

602

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over