Genetic Variant NM_007322.3:c.694-87A>G (chr19-5928174-T-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

18 publications found

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 was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007322.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RANBP3	NM_007322.3	MANE Select	c.694-87A>G	intron	N/A	NP_015561.1	Q9H6Z4-1
RANBP3	NM_003624.3		c.679-87A>G	intron	N/A	NP_003615.2	Q9H6Z4-2
RANBP3	NM_007320.3		c.490-87A>G	intron	N/A	NP_015559.2	Q9H6Z4-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RANBP3	ENST00000340578.10	TSL:1 MANE Select	c.694-87A>G	intron	N/A	ENSP00000341483.5	Q9H6Z4-1
RANBP3	ENST00000439268.6	TSL:1	c.679-87A>G	intron	N/A	ENSP00000404837.1	Q9H6Z4-2
RANBP3	ENST00000034275.12	TSL:1	c.490-87A>G	intron	N/A	ENSP00000034275.7	Q9H6Z4-3

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

African (AFR)

AF:

0.682

AC:

20364

AN:

29856

American (AMR)

AF:

0.836

AC:

28371

AN:

33928

Ashkenazi Jewish (ASJ)

AF:

0.686

AC:

14387

AN:

20962

East Asian (EAS)

AF:

0.736

AC:

28183

AN:

38272

South Asian (SAS)

AF:

0.738

AC:

52931

AN:

71690

European-Finnish (FIN)

AF:

0.555

AC:

22342

AN:

40288

Middle Eastern (MID)

AF:

0.722

AC:

3204

AN:

4436

European-Non Finnish (NFE)

AF:

0.689

AC:

714202

AN:

1036914

Other (OTH)

AF:

0.693

AC:

38392

AN:

55410

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

13142

26284

39425

52567

65709

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18582

37164

55746

74328

92910

<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:

0.681

AC:

103481

AN:

151952

Hom.:

35381

Cov.:

AF XY:

0.680

AC XY:

50528

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.673

AC:

27868

AN:

41426

American (AMR)

AF:

0.781

AC:

11926

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.692

AC:

2401

AN:

3470

East Asian (EAS)

AF:

0.734

AC:

3780

AN:

5150

South Asian (SAS)

AF:

0.748

AC:

3594

AN:

4808

European-Finnish (FIN)

AF:

0.535

AC:

5657

AN:

10564

Middle Eastern (MID)

AF:

0.684

AC:

201

AN:

294

European-Non Finnish (NFE)

AF:

0.678

AC:

46082

AN:

67950

Other (OTH)

AF:

0.682

AC:

1440

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1703

3407

5110

6814

8517

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

818

1636

2454

3272

4090

<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:

0.683

Hom.:

7606

Bravo

AF:

0.697

Asia WGS

AF:

0.720

AC:

2501

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.18

(source)

DANN

Benign

0.45

PhyloP100

-0.68

Mutation Taster

=12/88

disease causing

(source)

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

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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