chr5-170909677-C-G
Position:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_022897.5(RANBP17):āc.506C>Gā(p.Pro169Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00127 in 1,572,190 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00092 ( 0 hom., cov: 31)
Exomes š: 0.0013 ( 3 hom. )
Consequence
RANBP17
NM_022897.5 missense
NM_022897.5 missense
Scores
2
7
10
Clinical Significance
Conservation
PhyloP100: 6.74
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.11552614).
BP6
Variant 5-170909677-C-G is Benign according to our data. Variant chr5-170909677-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2656071.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RANBP17 | NM_022897.5 | c.506C>G | p.Pro169Arg | missense_variant | 6/28 | ENST00000523189.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RANBP17 | ENST00000523189.6 | c.506C>G | p.Pro169Arg | missense_variant | 6/28 | 1 | NM_022897.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000920 AC: 136AN: 147782Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
136
AN:
147782
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00103 AC: 251AN: 243908Hom.: 0 AF XY: 0.000991 AC XY: 131AN XY: 132134
GnomAD3 exomes
AF:
AC:
251
AN:
243908
Hom.:
AF XY:
AC XY:
131
AN XY:
132134
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00130 AC: 1856AN: 1424306Hom.: 3 Cov.: 26 AF XY: 0.00129 AC XY: 919AN XY: 710230
GnomAD4 exome
AF:
AC:
1856
AN:
1424306
Hom.:
Cov.:
26
AF XY:
AC XY:
919
AN XY:
710230
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000920 AC: 136AN: 147884Hom.: 0 Cov.: 31 AF XY: 0.000904 AC XY: 65AN XY: 71928
GnomAD4 genome
AF:
AC:
136
AN:
147884
Hom.:
Cov.:
31
AF XY:
AC XY:
65
AN XY:
71928
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
TwinsUK
AF:
AC:
5
ALSPAC
AF:
AC:
0
ESP6500AA
AF:
AC:
2
ESP6500EA
AF:
AC:
16
ExAC
AF:
AC:
125
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | RANBP17: BP4 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at