1-156068380-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020387.4(RAB25):c.350C>T(p.Thr117Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,614,104 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 (★).
Frequency
Consequence
NM_020387.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB25 | ENST00000361084.10 | c.350C>T | p.Thr117Met | missense_variant | Exon 3 of 5 | 1 | NM_020387.4 | ENSP00000354376.5 | ||
RAB25 | ENST00000497968.1 | n.169C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 1 | |||||
RAB25 | ENST00000473336.5 | n.172C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 | |||||
RAB25 | ENST00000487325.5 | n.349C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152102Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249594Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135410
GnomAD4 exome AF: 0.0000670 AC: 98AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.0000591 AC XY: 43AN XY: 727240
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.350C>T (p.T117M) alteration is located in exon 3 (coding exon 3) of the RAB25 gene. This alteration results from a C to T substitution at nucleotide position 350, causing the threonine (T) at amino acid position 117 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at