Variant rs950114 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018085.5(IPO9):c.2410-79T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 1,426,930 control chromosomes in the GnomAD database, including 3,027 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 0.035 ( 301 hom., cov: 31)

Exomes 𝑓: 0.037 ( 2726 hom. )

Consequence

IPO9
NM_018085.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.769

Variant links:

Genes affected

IPO9 (HGNC:19425): (importin 9) Enables nuclear import signal receptor activity. Involved in protein import into nucleus. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

IPO9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IPO9	NM_018085.5 linkuse as main transcript	c.2410-79T>C		intron_variant		ENST00000361565.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IPO9	ENST00000361565.9 linkuse as main transcript	c.2410-79T>C		intron_variant		1	NM_018085.5	P1

Frequencies

GnomAD3 genomes

AF:

0.0346

AC:

5265

AN:

152150

Hom.:

300

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0212

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0333

Gnomad ASJ

AF:

0.0793

Gnomad EAS

AF:

0.280

Gnomad SAS

AF:

0.0932

Gnomad FIN

AF:

0.00932

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0223

Gnomad OTH

AF:

0.0368

GnomAD4 exome

AF:

0.0368

AC:

46933

AN:

1274662

Hom.:

2726

Cov.:

AF XY:

0.0383

AC XY:

24355

AN XY:

635664

show subpopulations

Gnomad4 AFR exome

AF:

0.0228

Gnomad4 AMR exome

AF:

0.0556

Gnomad4 ASJ exome

AF:

0.0766

Gnomad4 EAS exome

AF:

0.310

Gnomad4 SAS exome

AF:

0.0875

Gnomad4 FIN exome

AF:

0.0127

Gnomad4 NFE exome

AF:

0.0214

Gnomad4 OTH exome

AF:

0.0453

GnomAD4 genome

AF:

0.0347

AC:

5280

AN:

152268

Hom.:

301

Cov.:

AF XY:

0.0372

AC XY:

2767

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0214

Gnomad4 AMR

AF:

0.0333

Gnomad4 ASJ

AF:

0.0793

Gnomad4 EAS

AF:

0.280

Gnomad4 SAS

AF:

0.0937

Gnomad4 FIN

AF:

0.00932

Gnomad4 NFE

AF:

0.0223

Gnomad4 OTH

AF:

0.0392

Alfa

AF:

0.0318

Hom.:

241

Bravo

AF:

0.0373

Asia WGS

AF:

0.169

AC:

588

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.10

DANN

Benign

0.35

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