14-21468733-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_032846.4(RAB2B):​c.206G>A​(p.Arg69His) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,552,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000016 ( 0 hom. )

Consequence

RAB2B
NM_032846.4 missense

Scores

8
9
2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.09
Variant links:
Genes affected
RAB2B (HGNC:20246): (RAB2B, member RAS oncogene family) Members of the Rab protein family are nontransforming monomeric GTP-binding proteins of the Ras superfamily that contain 4 highly conserved regions involved in GTP binding and hydrolysis. Rab proteins are prenylated, membrane-bound proteins involved in vesicular fusion and trafficking; see MIM 179508.[supplied by OMIM, Apr 2006]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.86

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RAB2BNM_032846.4 linkc.206G>A p.Arg69His missense_variant Exon 4 of 8 ENST00000397762.6 NP_116235.2 Q8WUD1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RAB2BENST00000397762.6 linkc.206G>A p.Arg69His missense_variant Exon 4 of 8 1 NM_032846.4 ENSP00000380869.1 Q8WUD1-1
RAB2BENST00000417141.5 linkn.187-4966G>A intron_variant Intron 3 of 5 1 ENSP00000405441.1 E9PE37
RAB2BENST00000649801.1 linkc.206G>A p.Arg69His missense_variant Exon 4 of 9 ENSP00000497782.1 A0A3B3ITL1
RAB2BENST00000461909.1 linkn.234G>A non_coding_transcript_exon_variant Exon 3 of 7 2

Frequencies

GnomAD3 genomes
AF:
0.0000132
AC:
2
AN:
151862
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000138
AC:
3
AN:
217148
Hom.:
0
AF XY:
0.0000169
AC XY:
2
AN XY:
118358
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000291
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000164
AC:
23
AN:
1400180
Hom.:
0
Cov.:
31
AF XY:
0.0000202
AC XY:
14
AN XY:
694192
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000585
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000194
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000132
AC:
2
AN:
151862
Hom.:
0
Cov.:
31
AF XY:
0.0000135
AC XY:
1
AN XY:
74118
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
May 06, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.206G>A (p.R69H) alteration is located in exon 4 (coding exon 4) of the RAB2B gene. This alteration results from a G to A substitution at nucleotide position 206, causing the arginine (R) at amino acid position 69 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.94
BayesDel_addAF
Pathogenic
0.30
D
BayesDel_noAF
Pathogenic
0.27
CADD
Pathogenic
26
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.58
D;.
Eigen
Uncertain
0.55
Eigen_PC
Uncertain
0.55
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Pathogenic
0.98
D;D
M_CAP
Benign
0.044
D
MetaRNN
Pathogenic
0.86
D;D
MetaSVM
Uncertain
0.069
D
MutationAssessor
Uncertain
2.1
M;.
PrimateAI
Uncertain
0.53
T
PROVEAN
Pathogenic
-4.5
D;.
REVEL
Pathogenic
0.78
Sift
Uncertain
0.013
D;.
Sift4G
Uncertain
0.019
D;.
Polyphen
0.99
D;.
Vest4
0.56
MutPred
0.80
Gain of catalytic residue at T72 (P = 5e-04);Gain of catalytic residue at T72 (P = 5e-04);
MVP
0.96
MPC
0.80
ClinPred
0.90
D
GERP RS
4.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.50
gMVP
0.39

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.14
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: rs747699476; hg19: chr14-21936892; API