Genetic Variant NM_014652.4:c.2109+24G>A (chr1-43960353-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.2109+24G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 1,605,036 control chromosomes in the GnomAD database, including 452,490 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 0.62 ( 32994 hom., cov: 31)

Exomes 𝑓: 0.75 ( 419496 hom. )

Consequence

IPO13
NM_014652.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

Publications

23 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=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
IPO13	NM_014652.4 link	c.2109+24G>A	intron_variant	Intron 12 of 19	ENST00000372343.8	NP_055467.3	O94829
IPO13	XM_024451069.2 link	c.1206+24G>A	intron_variant	Intron 11 of 18		XP_024306837.1
IPO13	XM_024451070.2 link	c.1206+24G>A	intron_variant	Intron 11 of 18		XP_024306838.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IPO13	ENST00000372343.8 link	c.2109+24G>A		intron_variant	Intron 12 of 19	1	NM_014652.4	ENSP00000361418.3		O94829

Frequencies

GnomAD3 genomes

AF:

0.625

AC:

94857

AN:

151838

Hom.:

32995

Cov.:

show subpopulations

Gnomad AFR

AF:

0.308

Gnomad AMI

AF:

0.871

Gnomad AMR

AF:

0.621

Gnomad ASJ

AF:

0.681

Gnomad EAS

AF:

0.625

Gnomad SAS

AF:

0.601

Gnomad FIN

AF:

0.780

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.788

Gnomad OTH

AF:

0.656

GnomAD2 exomes

AF:

0.683

AC:

171653

AN:

251172

AF XY:

0.693

show subpopulations

Gnomad AFR exome

AF:

0.299

Gnomad AMR exome

AF:

0.563

Gnomad ASJ exome

AF:

0.682

Gnomad EAS exome

AF:

0.644

Gnomad FIN exome

AF:

0.784

Gnomad NFE exome

AF:

0.783

Gnomad OTH exome

AF:

0.699

GnomAD4 exome

AF:

0.753

AC:

1093766

AN:

1453080

Hom.:

419496

Cov.:

AF XY:

0.750

AC XY:

542950

AN XY:

723484

show subpopulations

African (AFR)

AF:

0.287

AC:

9549

AN:

33254

American (AMR)

AF:

0.571

AC:

25520

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.686

AC:

17889

AN:

26078

East Asian (EAS)

AF:

0.572

AC:

22679

AN:

39636

South Asian (SAS)

AF:

0.614

AC:

52852

AN:

86016

European-Finnish (FIN)

AF:

0.785

AC:

41952

AN:

53408

Middle Eastern (MID)

AF:

0.611

AC:

3491

AN:

5712

European-Non Finnish (NFE)

AF:

0.794

AC:

876899

AN:

1104156

Other (OTH)

AF:

0.714

AC:

42935

AN:

60104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

13200

26400

39599

52799

65999

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20290

40580

60870

81160

101450

<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:

0.624

AC:

94878

AN:

151956

Hom.:

32994

Cov.:

AF XY:

0.622

AC XY:

46190

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.308

AC:

12749

AN:

41386

American (AMR)

AF:

0.621

AC:

9482

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.681

AC:

2363

AN:

3470

East Asian (EAS)

AF:

0.625

AC:

3229

AN:

5168

South Asian (SAS)

AF:

0.601

AC:

2895

AN:

4814

European-Finnish (FIN)

AF:

0.780

AC:

8240

AN:

10570

Middle Eastern (MID)

AF:

0.636

AC:

187

AN:

294

European-Non Finnish (NFE)

AF:

0.788

AC:

53555

AN:

67960

Other (OTH)

AF:

0.656

AC:

1384

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1504

3008

4512

6016

7520

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

756

1512

2268

3024

3780

<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:

0.738

Hom.:

28038

Bravo

AF:

0.602

Asia WGS

AF:

0.604

AC:

2101

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

9.4

(source)

DANN

Benign

0.75

PhyloP100

1.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over