rs3765133

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021252.5(RAB18):​c.187-55T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0271 in 1,276,490 control chromosomes in the GnomAD database, including 3,993 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 0.023 ( 314 hom., cov: 32)
Exomes 𝑓: 0.028 ( 3679 hom. )

Consequence

RAB18
NM_021252.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.449
Variant links:
Genes affected
RAB18 (HGNC:14244): (RAB18, member RAS oncogene family) The protein encoded by this gene is a member of a family of Ras-related small GTPases that regulate membrane trafficking in organelles and transport vesicles. Knockdown studies is zebrafish suggest that this protein may have a role in eye and brain development. Mutations in this gene are associated with Warburg micro syndrome type 3. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RAB18NM_021252.5 linkuse as main transcriptc.187-55T>A intron_variant ENST00000356940.11 NP_067075.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RAB18ENST00000356940.11 linkuse as main transcriptc.187-55T>A intron_variant 1 NM_021252.5 ENSP00000349415 P1Q9NP72-1

Frequencies

GnomAD3 genomes
AF:
0.0233
AC:
3535
AN:
152034
Hom.:
317
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00278
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0336
Gnomad ASJ
AF:
0.0150
Gnomad EAS
AF:
0.304
Gnomad SAS
AF:
0.142
Gnomad FIN
AF:
0.0318
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00306
Gnomad OTH
AF:
0.0225
GnomAD4 exome
AF:
0.0276
AC:
31025
AN:
1124338
Hom.:
3679
AF XY:
0.0302
AC XY:
17375
AN XY:
574978
show subpopulations
Gnomad4 AFR exome
AF:
0.00167
Gnomad4 AMR exome
AF:
0.0502
Gnomad4 ASJ exome
AF:
0.0157
Gnomad4 EAS exome
AF:
0.378
Gnomad4 SAS exome
AF:
0.116
Gnomad4 FIN exome
AF:
0.0316
Gnomad4 NFE exome
AF:
0.00242
Gnomad4 OTH exome
AF:
0.0310
GnomAD4 genome
AF:
0.0232
AC:
3530
AN:
152152
Hom.:
314
Cov.:
32
AF XY:
0.0283
AC XY:
2108
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.00277
Gnomad4 AMR
AF:
0.0338
Gnomad4 ASJ
AF:
0.0150
Gnomad4 EAS
AF:
0.304
Gnomad4 SAS
AF:
0.141
Gnomad4 FIN
AF:
0.0318
Gnomad4 NFE
AF:
0.00306
Gnomad4 OTH
AF:
0.0213
Alfa
AF:
0.0112
Hom.:
8
Bravo
AF:
0.0228
Asia WGS
AF:
0.195
AC:
673
AN:
3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
14
DANN
Benign
0.74

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: rs3765133; hg19: chr10-27821381; COSMIC: COSV63613255; API