chr5-170909677-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_022897.5(RANBP17):ā€‹c.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

Scores

2
7
10

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.74
Variant links:
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
RANBP17NM_022897.5 linkuse as main transcriptc.506C>G p.Pro169Arg missense_variant 6/28 ENST00000523189.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RANBP17ENST00000523189.6 linkuse as main transcriptc.506C>G p.Pro169Arg missense_variant 6/281 NM_022897.5 P1Q9H2T7-1

Frequencies

GnomAD3 genomes
AF:
0.000920
AC:
136
AN:
147782
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000150
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00199
Gnomad ASJ
AF:
0.00145
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000212
Gnomad FIN
AF:
0.000515
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00130
Gnomad OTH
AF:
0.00149
GnomAD3 exomes
AF:
0.00103
AC:
251
AN:
243908
Hom.:
0
AF XY:
0.000991
AC XY:
131
AN XY:
132134
show subpopulations
Gnomad AFR exome
AF:
0.000129
Gnomad AMR exome
AF:
0.00112
Gnomad ASJ exome
AF:
0.00141
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000475
Gnomad FIN exome
AF:
0.000561
Gnomad NFE exome
AF:
0.00147
Gnomad OTH exome
AF:
0.00153
GnomAD4 exome
AF:
0.00130
AC:
1856
AN:
1424306
Hom.:
3
Cov.:
26
AF XY:
0.00129
AC XY:
919
AN XY:
710230
show subpopulations
Gnomad4 AFR exome
AF:
0.000374
Gnomad4 AMR exome
AF:
0.00136
Gnomad4 ASJ exome
AF:
0.00144
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000370
Gnomad4 FIN exome
AF:
0.000644
Gnomad4 NFE exome
AF:
0.00149
Gnomad4 OTH exome
AF:
0.00102
GnomAD4 genome
AF:
0.000920
AC:
136
AN:
147884
Hom.:
0
Cov.:
31
AF XY:
0.000904
AC XY:
65
AN XY:
71928
show subpopulations
Gnomad4 AFR
AF:
0.000150
Gnomad4 AMR
AF:
0.00199
Gnomad4 ASJ
AF:
0.00145
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000212
Gnomad4 FIN
AF:
0.000515
Gnomad4 NFE
AF:
0.00130
Gnomad4 OTH
AF:
0.00147
Alfa
AF:
0.00125
Hom.:
0
TwinsUK
AF:
0.00135
AC:
5
ALSPAC
AF:
0.00
AC:
0
ESP6500AA
AF:
0.000454
AC:
2
ESP6500EA
AF:
0.00186
AC:
16
ExAC
AF:
0.00103
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 submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2023RANBP17: BP4 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.73
BayesDel_addAF
Benign
-0.20
T
BayesDel_noAF
Benign
-0.10
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Benign
0.069
T
Eigen
Uncertain
0.51
Eigen_PC
Uncertain
0.58
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.87
D
M_CAP
Benign
0.020
T
MetaRNN
Benign
0.12
T
MetaSVM
Benign
-0.49
T
MutationAssessor
Benign
1.9
L
MutationTaster
Benign
1.0
D
PrimateAI
Benign
0.48
T
PROVEAN
Uncertain
-3.3
D
REVEL
Benign
0.24
Sift
Uncertain
0.0050
D
Sift4G
Uncertain
0.017
D
Polyphen
0.96
D
Vest4
0.73
MVP
0.83
MPC
0.078
ClinPred
0.081
T
GERP RS
5.4
Varity_R
0.27
gMVP
0.26

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs139178386; hg19: chr5-170336681; API