chr14-64951099-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001308154.2(RAB15):ā€‹c.299T>Cā€‹(p.Met100Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,460,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000027 ( 0 hom. )

Consequence

RAB15
NM_001308154.2 missense

Scores

2
6
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.45
Variant links:
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 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.33624256).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RAB15NM_001308154.2 linkuse as main transcriptc.299T>C p.Met100Thr missense_variant 4/7 ENST00000533601.7 NP_001295083.1
CHURC1-FNTBNM_001202559.1 linkuse as main transcriptc.327+25019A>G intron_variant NP_001189488.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RAB15ENST00000533601.7 linkuse as main transcriptc.299T>C p.Met100Thr missense_variant 4/71 NM_001308154.2 ENSP00000434103 P1P59190-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000274
AC:
4
AN:
1460770
Hom.:
0
Cov.:
31
AF XY:
0.00000550
AC XY:
4
AN XY:
726790
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
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:
0.00000360
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

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 submitterclinical testingAmbry GeneticsMay 17, 2023The c.299T>C (p.M100T) alteration is located in exon 4 (coding exon 4) of the RAB15 gene. This alteration results from a T to C substitution at nucleotide position 299, causing the methionine (M) at amino acid position 100 to be replaced by a threonine (T). 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
Benign
0.27
BayesDel_addAF
Pathogenic
0.25
D
BayesDel_noAF
Uncertain
0.12
CADD
Benign
22
DANN
Benign
0.95
DEOGEN2
Benign
0.16
.;T;T;.;.;.
Eigen
Uncertain
0.37
Eigen_PC
Uncertain
0.49
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.92
D;T;T;T;T;D
M_CAP
Benign
0.080
D
MetaRNN
Benign
0.34
T;T;T;T;T;T
MetaSVM
Benign
-0.45
T
MutationAssessor
Benign
-1.1
N;N;.;.;.;.
MutationTaster
Benign
1.0
D;D;N;N;N;N
PrimateAI
Pathogenic
0.83
D
PROVEAN
Benign
-0.27
N;N;N;.;.;.
REVEL
Uncertain
0.40
Sift
Benign
0.096
T;T;T;.;.;.
Sift4G
Benign
0.14
T;T;.;.;.;.
Polyphen
0.99
D;.;.;.;.;.
Vest4
0.54
MutPred
0.32
Loss of stability (P = 0.0397);Loss of stability (P = 0.0397);.;.;.;.;
MVP
0.93
MPC
0.86
ClinPred
0.87
D
GERP RS
5.6
Varity_R
0.15
gMVP
0.73

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-65417817; API