chr5-171213458-A-G

Variant names:

• chr5-171213458-A-G
• rs4868073
• NM_022897.5:c.2232-173A>G

Variant summary

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

The NM_022897.5(RANBP17):​c.2232-173A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,998 control chromosomes in the GnomAD database, including 26,241 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 0.58 (26241 hom., cov: 32)
• Consequence: RANBP17 NM_022897.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 2 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RANBP17	NM_022897.5	c.2232-173A>G		intron_variant	Intron 20 of 27	ENST00000523189.6	NP_075048.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RANBP17	ENST00000523189.6	c.2232-173A>G		intron_variant	Intron 20 of 27	1	NM_022897.5	ENSP00000427975.1

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87438 AN: 151882 Hom.: 26238 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.575 AC: 87458 AN: 151998 Hom.: 26241 Cov.: 32 AF XY: 0.582 AC XY: 43199 AN XY: 74264

African (AFR) AF: 0.390 AC: 16162 AN: 41478

American (AMR) AF: 0.628 AC: 9567 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2121 AN: 3470

East Asian (EAS) AF: 0.717 AC: 3712 AN: 5180

South Asian (SAS) AF: 0.764 AC: 3669 AN: 4802

European-Finnish (FIN) AF: 0.636 AC: 6712 AN: 10548

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43389 AN: 67970

Other (OTH) AF: 0.584 AC: 1228 AN: 2104

Alfa AF: 0.603 Hom.: 14520

Bravo AF: 0.563

Asia WGS AF: 0.668 AC: 2321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	6.7
DANN	Benign	0.62
PhyloP100		1.1
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: rs4868073; hg19: chr5-170640462; COSMIC: COSV66647965;