19-5961872-G-C

Position:

• chr19-5961872-G-C

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RANBP3	NM_007322.3	c.23-3899C>G		intron_variant		ENST00000340578.10	NP_015561.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RANBP3	ENST00000340578.10	c.23-3899C>G		intron_variant		1	NM_007322.3	ENSP00000341483.5

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

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.704

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.70

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

Other links and lift over

dbSNP: rs551244; hg19: chr19-5961883;