dbSNP rs2906596: IPO13:c.2344+14G>A (chr1-43961276-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014652.4(IPO13):c.2344+14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 1,603,624 control chromosomes in the GnomAD database, including 665,196 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 0.86 ( 56468 hom., cov: 32)

Exomes 𝑓: 0.91 ( 608728 hom. )

Consequence

IPO13
NM_014652.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.121

Publications

15 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
IPO13	NM_014652.4 link	c.2344+14G>A	intron_variant	Intron 14 of 19	ENST00000372343.8	NP_055467.3	O94829
IPO13	XM_024451069.2 link	c.1441+14G>A	intron_variant	Intron 13 of 18		XP_024306837.1
IPO13	XM_024451070.2 link	c.1441+14G>A	intron_variant	Intron 13 of 18		XP_024306838.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IPO13	ENST00000372343.8 link	c.2344+14G>A		intron_variant	Intron 14 of 19	1	NM_014652.4	ENSP00000361418.3		O94829

Frequencies

GnomAD3 genomes

AF:

0.856

AC:

130163

AN:

152048

Hom.:

56447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.708

Gnomad AMI

AF:

0.985

Gnomad AMR

AF:

0.872

Gnomad ASJ

AF:

0.928

Gnomad EAS

AF:

0.834

Gnomad SAS

AF:

0.904

Gnomad FIN

AF:

0.875

Gnomad MID

AF:

0.829

Gnomad NFE

AF:

0.932

Gnomad OTH

AF:

0.866

GnomAD2 exomes

AF:

0.889

AC:

223284

AN:

251222

AF XY:

0.895

show subpopulations

Gnomad AFR exome

AF:

0.706

Gnomad AMR exome

AF:

0.848

Gnomad ASJ exome

AF:

0.929

Gnomad EAS exome

AF:

0.848

Gnomad FIN exome

AF:

0.883

Gnomad NFE exome

AF:

0.928

Gnomad OTH exome

AF:

0.893

GnomAD4 exome

AF:

0.915

AC:

1327551

AN:

1451458

Hom.:

608728

Cov.:

AF XY:

0.915

AC XY:

661721

AN XY:

722874

show subpopulations

African (AFR)

AF:

0.698

AC:

23171

AN:

33206

American (AMR)

AF:

0.850

AC:

38000

AN:

44704

Ashkenazi Jewish (ASJ)

AF:

0.928

AC:

24195

AN:

26064

East Asian (EAS)

AF:

0.800

AC:

31686

AN:

39632

South Asian (SAS)

AF:

0.899

AC:

77358

AN:

86054

European-Finnish (FIN)

AF:

0.885

AC:

47194

AN:

53300

Middle Eastern (MID)

AF:

0.867

AC:

4976

AN:

5742

European-Non Finnish (NFE)

AF:

0.931

AC:

1026957

AN:

1102714

Other (OTH)

AF:

0.900

AC:

54014

AN:

60042

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

6276

12552

18827

25103

31379

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21278

42556

63834

85112

106390

<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:

0.856

AC:

130239

AN:

152166

Hom.:

56468

Cov.:

AF XY:

0.855

AC XY:

63582

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.708

AC:

29362

AN:

41464

American (AMR)

AF:

0.872

AC:

13339

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.928

AC:

3222

AN:

3472

East Asian (EAS)

AF:

0.834

AC:

4320

AN:

5182

South Asian (SAS)

AF:

0.903

AC:

4351

AN:

4816

European-Finnish (FIN)

AF:

0.875

AC:

9279

AN:

10608

Middle Eastern (MID)

AF:

0.827

AC:

243

AN:

294

European-Non Finnish (NFE)

AF:

0.932

AC:

63395

AN:

68018

Other (OTH)

AF:

0.867

AC:

1832

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

887

1774

2661

3548

4435

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

890

1780

2670

3560

4450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.894

Hom.:

22527

Bravo

AF:

0.849

Asia WGS

AF:

0.860

AC:

2991

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

6.1

(source)

DANN

Benign

0.76

PhyloP100

-0.12

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over