22-23155487-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004914.5(RAB36):c.330-481T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,150 control chromosomes in the GnomAD database, including 48,490 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 0.80 ( 48490 hom., cov: 33)
Consequence
RAB36
NM_004914.5 intron
NM_004914.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.194
Publications
11 publications found
Genes affected
RAB36 (HGNC:9775): (RAB36, member RAS oncogene family) Predicted to enable GTP binding activity and GTPase activity. Predicted to be involved in protein transport. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]
RSPH14 (HGNC:13437): (radial spoke head 14 homolog) This gene encodes a protein with no known function but with slight similarity to a yeast vacuolar protein. The gene is located in a region deleted in pediatric rhabdoid tumors of the brain, kidney and soft tissues, but mutations in this gene have not been associated with the disease. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB36 | ENST00000263116.8 | c.330-481T>C | intron_variant | Intron 5 of 10 | 1 | NM_004914.5 | ENSP00000263116.3 | |||
RAB36 | ENST00000341989.9 | c.264-481T>C | intron_variant | Intron 4 of 9 | 1 | ENSP00000343494.5 | ||||
RAB36 | ENST00000420895.1 | c.210-481T>C | intron_variant | Intron 3 of 3 | 3 | ENSP00000397594.1 |
Frequencies
GnomAD3 genomes AF: 0.796 AC: 121010AN: 152032Hom.: 48437 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
121010
AN:
152032
Hom.:
Cov.:
33
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.796 AC: 121122AN: 152150Hom.: 48490 Cov.: 33 AF XY: 0.798 AC XY: 59384AN XY: 74370 show subpopulations
GnomAD4 genome
AF:
AC:
121122
AN:
152150
Hom.:
Cov.:
33
AF XY:
AC XY:
59384
AN XY:
74370
show subpopulations
African (AFR)
AF:
AC:
35368
AN:
41522
American (AMR)
AF:
AC:
12328
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
2532
AN:
3470
East Asian (EAS)
AF:
AC:
5114
AN:
5160
South Asian (SAS)
AF:
AC:
3836
AN:
4818
European-Finnish (FIN)
AF:
AC:
7684
AN:
10586
Middle Eastern (MID)
AF:
AC:
228
AN:
294
European-Non Finnish (NFE)
AF:
AC:
51693
AN:
67988
Other (OTH)
AF:
AC:
1638
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1239
2478
3716
4955
6194
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
870
1740
2610
3480
4350
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3085
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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