5-171293729-C-G

Position:

• chr5-171293729-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022897.5(RANBP17):​c.2944-154C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 152,226 control chromosomes in the GnomAD database, including 299 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 0.056 (299 hom., cov: 33)
• Consequence: RANBP17 NM_022897.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

Genes affected

RANBP17 (HGNC:14428): (RAN binding protein 17) The transport of protein and large RNAs through the nuclear pore complexes (NPC) is an energy-dependent and regulated process. The import of proteins with a nuclear localization signal (NLS) is accomplished by recognition of one or more clusters of basic amino acids by the importin-alpha/beta complex; see MIM 600685 and MIM 602738. The small GTPase RAN (MIM 601179) plays a key role in NLS-dependent protein import. RAN-binding protein-17 is a member of the importin-beta superfamily of nuclear transport receptors.[supplied by OMIM, Jul 2002]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RANBP17	NM_022897.5	c.2944-154C>G		intron_variant		ENST00000523189.6	NP_075048.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RANBP17	ENST00000523189.6	c.2944-154C>G		intron_variant		1	NM_022897.5	ENSP00000427975.1

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8461 AN: 152108 Hom.: 298 Cov.: 33

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0429

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0598

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0556 AC: 8464 AN: 152226 Hom.: 299 Cov.: 33 AF XY: 0.0542 AC XY: 4031 AN XY: 74412

Gnomad4 AFR AF: 0.0471

Gnomad4 AMR AF: 0.0568

Gnomad4 ASJ AF: 0.0663

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.0429

Gnomad4 NFE AF: 0.0599

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0611 Hom.: 157

Bravo AF: 0.0571

Asia WGS AF: 0.0620 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.24
DANN	Benign	0.63

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: rs2278255; hg19: chr5-170720733;