NM_007322.3:c.23-3899C>G

Variant names:

• chr19-5961872-G-C
• rs551244
• NM_007322.3:c.23-3899C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007322.3(RANBP3):​c.23-3899C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 151,640 control chromosomes in the GnomAD database, including 38,494 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 0.71 (38494 hom., cov: 29)
• Consequence: RANBP3 NM_007322.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 11 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.778 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RANBP3	NM_007322.3	MANE Select	c.23-3899C>G		intron	N/A	NP_015561.1
	RANBP3	NM_003624.3		c.23-3899C>G		intron	N/A	NP_003615.2
	RANBP3	NM_007320.3		c.23-3899C>G		intron	N/A	NP_015559.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RANBP3	ENST00000340578.10	TSL:1 MANE Select	c.23-3899C>G		intron	N/A	ENSP00000341483.5
	RANBP3	ENST00000439268.6	TSL:1	c.23-3899C>G		intron	N/A	ENSP00000404837.1
	RANBP3	ENST00000034275.12	TSL:1	c.23-3899C>G		intron	N/A	ENSP00000034275.7

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107508 AN: 151522 Hom.: 38446 Cov.: 29

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.702

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.710 AC: 107614 AN: 151640 Hom.: 38494 Cov.: 29 AF XY: 0.708 AC XY: 52428 AN XY: 74076

African (AFR) AF: 0.774 AC: 31961 AN: 41284

American (AMR) AF: 0.789 AC: 12053 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2389 AN: 3462

East Asian (EAS) AF: 0.727 AC: 3719 AN: 5114

South Asian (SAS) AF: 0.748 AC: 3594 AN: 4804

European-Finnish (FIN) AF: 0.536 AC: 5632 AN: 10498

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46047 AN: 67900

Other (OTH) AF: 0.704 AC: 1481 AN: 2104

Alfa AF: 0.683 Hom.: 4431

Bravo AF: 0.729

Asia WGS AF: 0.732 AC: 2546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.70
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs551244; hg19: chr19-5961883;