Variant 1-43956950-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2

The NM_014652.4(IPO13):c.1245C>T(p.Asp415=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0344 in 1,614,084 control chromosomes in the GnomAD database, including 1,069 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 0.027 ( 67 hom., cov: 32)

Exomes 𝑓: 0.035 ( 1002 hom. )

Consequence

IPO13
NM_014652.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0620

Variant links:

Genes affected

IPO13 (HGNC:16853): (importin 13) This gene encodes a member of the importin-beta family of nuclear transport proteins. The encoded protein mediates the import of specific cargo proteins from the cytoplasm to the nucleus and is dependent on the Ras-related nuclear protein-GTPase system. The encoded protein is also involved in nuclear export of the eukaryotic translation initiation factor 1A.[provided by RefSeq, Mar 2009]

IPO13 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP7

Synonymous conserved (PhyloP=-0.062 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0272 (4139/152344) while in subpopulation NFE AF= 0.0395 (2690/68034). AF 95% confidence interval is 0.0383. There are 67 homozygotes in gnomad4. There are 1958 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 4139 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
IPO13	NM_014652.4 linkuse as main transcript	c.1245C>T	p.Asp415=	synonymous_variant	5/20	ENST00000372343.8
IPO13	XM_024451069.2 linkuse as main transcript	c.342C>T	p.Asp114=	synonymous_variant	4/19
IPO13	XM_024451070.2 linkuse as main transcript	c.342C>T	p.Asp114=	synonymous_variant	4/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IPO13	ENST00000372343.8 linkuse as main transcript	c.1245C>T	p.Asp415=	synonymous_variant	5/20	1	NM_014652.4	P1
IPO13	ENST00000492152.5 linkuse as main transcript	n.691C>T		non_coding_transcript_exon_variant	4/6	3

Frequencies

GnomAD3 genomes

AF:

0.0272

AC:

4142

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00646

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0320

Gnomad ASJ

AF:

0.0294

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0329

Gnomad FIN

AF:

0.0328

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0395

Gnomad OTH

AF:

0.0296

GnomAD3 exomes

AF:

0.0287

AC:

7198

AN:

251110

Hom.:

136

AF XY:

0.0297

AC XY:

4034

AN XY:

135762

show subpopulations

Gnomad AFR exome

AF:

0.00653

Gnomad AMR exome

AF:

0.0175

Gnomad ASJ exome

AF:

0.0249

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0285

Gnomad FIN exome

AF:

0.0332

Gnomad NFE exome

AF:

0.0393

Gnomad OTH exome

AF:

0.0293

GnomAD4 exome

AF:

0.0352

AC:

51381

AN:

1461740

Hom.:

1002

Cov.:

AF XY:

0.0351

AC XY:

25515

AN XY:

727178

show subpopulations

Gnomad4 AFR exome

AF:

0.00580

Gnomad4 AMR exome

AF:

0.0174

Gnomad4 ASJ exome

AF:

0.0259

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0309

Gnomad4 FIN exome

AF:

0.0349

Gnomad4 NFE exome

AF:

0.0387

Gnomad4 OTH exome

AF:

0.0323

GnomAD4 genome

AF:

0.0272

AC:

4139

AN:

152344

Hom.:

Cov.:

AF XY:

0.0263

AC XY:

1958

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00645

Gnomad4 AMR

AF:

0.0319

Gnomad4 ASJ

AF:

0.0294

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0327

Gnomad4 FIN

AF:

0.0328

Gnomad4 NFE

AF:

0.0395

Gnomad4 OTH

AF:

0.0293

Alfa

AF:

0.0301

Hom.:

Bravo

AF:

0.0255

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.0429

EpiControl

AF:

0.0373

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

6.7

DANN

Benign

0.51

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over