dbSNP rs2301992: IPO13:c.2248-15C>T (chr1-43961151-C-T) – 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.2248-15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0523 in 1,611,952 control chromosomes in the GnomAD database, including 3,077 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 0.077 ( 684 hom., cov: 33)

Exomes 𝑓: 0.050 ( 2393 hom. )

Consequence

IPO13
NM_014652.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.368

Publications

16 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:

Genome browser will be placed here

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=-0.7).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014652.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IPO13	NM_014652.4	MANE Select	c.2248-15C>T		intron	N/A	NP_055467.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IPO13	ENST00000372343.8	TSL:1 MANE Select	c.2248-15C>T	intron	N/A	ENSP00000361418.3	O94829
IPO13	ENST00000862671.1		c.2317-15C>T	intron	N/A	ENSP00000532730.1
IPO13	ENST00000862663.1		c.2266-15C>T	intron	N/A	ENSP00000532722.1

Frequencies

GnomAD3 genomes

AF:

0.0773

AC:

11747

AN:

152062

Hom.:

684

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.00989

Gnomad AMR

AF:

0.0666

Gnomad ASJ

AF:

0.0262

Gnomad EAS

AF:

0.113

Gnomad SAS

AF:

0.0964

Gnomad FIN

AF:

0.0206

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0413

Gnomad OTH

AF:

0.0690

GnomAD2 exomes

AF:

0.0617

AC:

15510

AN:

251440

AF XY:

0.0606

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.0667

Gnomad ASJ exome

AF:

0.0231

Gnomad EAS exome

AF:

0.112

Gnomad FIN exome

AF:

0.0226

Gnomad NFE exome

AF:

0.0404

Gnomad OTH exome

AF:

0.0559

GnomAD4 exome

AF:

0.0497

AC:

72534

AN:

1459772

Hom.:

2393

Cov.:

AF XY:

0.0504

AC XY:

36642

AN XY:

726360

show subpopulations

African (AFR)

AF:

0.159

AC:

5308

AN:

33440

American (AMR)

AF:

0.0646

AC:

2888

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0240

AC:

626

AN:

26120

East Asian (EAS)

AF:

0.128

AC:

5083

AN:

39690

South Asian (SAS)

AF:

0.0928

AC:

8001

AN:

86204

European-Finnish (FIN)

AF:

0.0230

AC:

1230

AN:

53418

Middle Eastern (MID)

AF:

0.0484

AC:

279

AN:

5764

European-Non Finnish (NFE)

AF:

0.0412

AC:

45763

AN:

1110068

Other (OTH)

AF:

0.0556

AC:

3356

AN:

60346

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

3865

7730

11595

15460

19325

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1926

3852

5778

7704

9630

<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:

0.0773

AC:

11759

AN:

152180

Hom.:

684

Cov.:

AF XY:

0.0773

AC XY:

5749

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.154

AC:

6396

AN:

41494

American (AMR)

AF:

0.0669

AC:

1024

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0262

AC:

AN:

3468

East Asian (EAS)

AF:

0.113

AC:

583

AN:

5164

South Asian (SAS)

AF:

0.0961

AC:

463

AN:

4818

European-Finnish (FIN)

AF:

0.0206

AC:

219

AN:

10616

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0413

AC:

2810

AN:

68008

Other (OTH)

AF:

0.0716

AC:

151

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

544

1088

1632

2176

2720

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

264

396

528

660

<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:

0.0519

Hom.:

386

Bravo

AF:

0.0821

Asia WGS

AF:

0.112

AC:

391

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.51

PhyloP100

0.37

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over