chr14-64951121-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001308154.2(RAB15):c.277G>A(p.Glu93Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000685 in 1,460,446 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
RAB15
NM_001308154.2 missense
NM_001308154.2 missense
Scores
4
10
5
Clinical Significance
Conservation
PhyloP100: 7.06
Genes affected
RAB15 (HGNC:20150): (RAB15, member RAS oncogene family) Predicted to enable GTP binding activity and GTPase activity. Involved in positive regulation of regulated secretory pathway. Located in cilium; endosome membrane; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAB15 | NM_001308154.2 | c.277G>A | p.Glu93Lys | missense_variant | 4/7 | ENST00000533601.7 | NP_001295083.1 | |
CHURC1-FNTB | NM_001202559.1 | c.327+25041C>T | intron_variant | NP_001189488.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB15 | ENST00000533601.7 | c.277G>A | p.Glu93Lys | missense_variant | 4/7 | 1 | NM_001308154.2 | ENSP00000434103 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249870Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135202
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GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460446Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726630
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 19, 2024 | The c.277G>A (p.E93K) alteration is located in exon 4 (coding exon 4) of the RAB15 gene. This alteration results from a G to A substitution at nucleotide position 277, causing the glutamic acid (E) at amino acid position 93 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
.;T;T;.;.;.
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Benign
N;N;.;.;.;.
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D;.;.;.
REVEL
Uncertain
Sift
Benign
D;D;T;.;.;.
Sift4G
Benign
T;T;.;.;.;.
Polyphen
D;.;.;.;.;.
Vest4
MutPred
Gain of MoRF binding (P = 0.0027);Gain of MoRF binding (P = 0.0027);.;.;.;.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at