Variant rs274793 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_007322.3(RANBP3):c.694-87A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 1,483,708 control chromosomes in the GnomAD database, including 356,156 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 0.68 ( 35381 hom., cov: 31)

Exomes 𝑓: 0.69 ( 320775 hom. )

Consequence

RANBP3
NM_007322.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.682

Variant links:

Genes affected

RANBP3 (HGNC:9850): (RAN binding protein 3) This gene encodes a protein with a RanBD1 domain that is found in both the nucleus and cytoplasm. This protein plays a role in nuclear export as part of a heteromeric complex. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

RANBP3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RANBP3	NM_007322.3 linkuse as main transcript	c.694-87A>G		intron_variant		ENST00000340578.10	NP_015561.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RANBP3	ENST00000340578.10 linkuse as main transcript	c.694-87A>G		intron_variant		1	NM_007322.3	ENSP00000341483	P3	Q9H6Z4-1

Frequencies

GnomAD3 genomes

AF:

0.681

AC:

103396

AN:

151834

Hom.:

35350

Cov.:

show subpopulations

Gnomad AFR

AF:

0.673

Gnomad AMI

AF:

0.585

Gnomad AMR

AF:

0.781

Gnomad ASJ

AF:

0.692

Gnomad EAS

AF:

0.734

Gnomad SAS

AF:

0.747

Gnomad FIN

AF:

0.535

Gnomad MID

AF:

0.687

Gnomad NFE

AF:

0.678

Gnomad OTH

AF:

0.682

GnomAD4 exome

AF:

0.693

AC:

922376

AN:

1331756

Hom.:

320775

Cov.:

AF XY:

0.693

AC XY:

456690

AN XY:

659200

show subpopulations

Gnomad4 AFR exome

AF:

0.682

Gnomad4 AMR exome

AF:

0.836

Gnomad4 ASJ exome

AF:

0.686

Gnomad4 EAS exome

AF:

0.736

Gnomad4 SAS exome

AF:

0.738

Gnomad4 FIN exome

AF:

0.555

Gnomad4 NFE exome

AF:

0.689

Gnomad4 OTH exome

AF:

0.693

GnomAD4 genome

AF:

0.681

AC:

103481

AN:

151952

Hom.:

35381

Cov.:

AF XY:

0.680

AC XY:

50528

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.673

Gnomad4 AMR

AF:

0.781

Gnomad4 ASJ

AF:

0.692

Gnomad4 EAS

AF:

0.734

Gnomad4 SAS

AF:

0.748

Gnomad4 FIN

AF:

0.535

Gnomad4 NFE

AF:

0.678

Gnomad4 OTH

AF:

0.682

Alfa

AF:

0.683

Hom.:

7433

Bravo

AF:

0.697

Asia WGS

AF:

0.720

AC:

2501

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.18

DANN

Benign

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.21

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.21

Position offset: 5

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