rs2604894
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016154.5(RAB4B):c.431-166A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 989,550 control chromosomes in the GnomAD database, including 153,208 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 0.55 ( 23218 hom., cov: 29)
Exomes 𝑓: 0.55 ( 129990 hom. )
Consequence
RAB4B
NM_016154.5 intron
NM_016154.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.295
Genes affected
RAB4B (HGNC:9782): (RAB4B, member RAS oncogene family) Predicted to enable G protein activity and GTP binding activity. Involved in glucose import. Located in insulin-responsive compartment; perinuclear region of cytoplasm; and recycling endosome. [provided by Alliance of Genome Resources, Apr 2022]
RAB4B-EGLN2 (HGNC:44465): (RAB4B-EGLN2 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring RAB4B (RAB4B, member RAS oncogene family) and EGLN2 (egl nine homolog 2) genes on chromosome 19. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]
MIA-RAB4B (HGNC:48352): (MIA-RAB4B readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring MIA (melanoma inhibitory activity) and RAB4B (RAB4B, member RAS oncogene family) genes on chromosome 19. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is therefore unlikely to produce a protein product. [provided by RefSeq, Feb 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAB4B | NM_016154.5 | c.431-166A>G | intron_variant | ENST00000357052.8 | NP_057238.3 | |||
MIA-RAB4B | NR_037775.1 | n.793-166A>G | intron_variant | |||||
RAB4B-EGLN2 | NR_037791.1 | n.588-166A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB4B | ENST00000357052.8 | c.431-166A>G | intron_variant | 1 | NM_016154.5 | ENSP00000349560.2 | ||||
RAB4B-EGLN2 | ENST00000594136.2 | n.431-166A>G | intron_variant | 2 | ENSP00000469872.1 | |||||
MIA-RAB4B | ENST00000600729.2 | n.*391-166A>G | intron_variant | 5 | ENSP00000472384.1 |
Frequencies
GnomAD3 genomes AF: 0.549 AC: 83145AN: 151548Hom.: 23189 Cov.: 29
GnomAD3 genomes
AF:
AC:
83145
AN:
151548
Hom.:
Cov.:
29
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:
GnomAD4 exome AF: 0.553 AC: 463743AN: 837882Hom.: 129990 Cov.: 11 AF XY: 0.547 AC XY: 230197AN XY: 420726
GnomAD4 exome
AF:
AC:
463743
AN:
837882
Hom.:
Cov.:
11
AF XY:
AC XY:
230197
AN XY:
420726
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: 0.549 AC: 83225AN: 151668Hom.: 23218 Cov.: 29 AF XY: 0.551 AC XY: 40837AN XY: 74084
GnomAD4 genome
AF:
AC:
83225
AN:
151668
Hom.:
Cov.:
29
AF XY:
AC XY:
40837
AN XY:
74084
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.:
Bravo
AF:
Asia WGS
AF:
AC:
2039
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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