Variant rs1400875 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.603+123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 595,946 control chromosomes in the GnomAD database, including 26,832 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 0.28 ( 6255 hom., cov: 32)

Exomes 𝑓: 0.29 ( 20577 hom. )

Consequence

IPO9
NM_018085.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.565

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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IPO9	NM_018085.5 linkuse as main transcript	c.603+123T>C		intron_variant		ENST00000361565.9	NP_060555.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IPO9	ENST00000361565.9 linkuse as main transcript	c.603+123T>C		intron_variant		1	NM_018085.5	ENSP00000354742	P1
IPO9	ENST00000464348.5 linkuse as main transcript	n.775+123T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42712

AN:

151950

Hom.:

6251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.354

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.190

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.269

Gnomad FIN

AF:

0.314

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.329

Gnomad OTH

AF:

0.251

GnomAD4 exome

AF:

0.293

AC:

129926

AN:

443876

Hom.:

20577

AF XY:

0.293

AC XY:

68643

AN XY:

234352

show subpopulations

Gnomad4 AFR exome

AF:

0.230

Gnomad4 AMR exome

AF:

0.258

Gnomad4 ASJ exome

AF:

0.192

Gnomad4 EAS exome

AF:

0.102

Gnomad4 SAS exome

AF:

0.286

Gnomad4 FIN exome

AF:

0.299

Gnomad4 NFE exome

AF:

0.327

Gnomad4 OTH exome

AF:

0.281

GnomAD4 genome

AF:

0.281

AC:

42730

AN:

152070

Hom.:

6255

Cov.:

AF XY:

0.279

AC XY:

20719

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.230

Gnomad4 AMR

AF:

0.268

Gnomad4 ASJ

AF:

0.190

Gnomad4 EAS

AF:

0.103

Gnomad4 SAS

AF:

0.268

Gnomad4 FIN

AF:

0.314

Gnomad4 NFE

AF:

0.329

Gnomad4 OTH

AF:

0.249

Alfa

AF:

0.313

Hom.:

3699

Bravo

AF:

0.275

Asia WGS

AF:

0.163

AC:

564

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

8.2

DANN

Benign

0.66

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