18-8609764-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001025300.3(RAB12):c.325G>A(p.Gly109Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000122 in 1,268,312 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001025300.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAB12 | NM_001025300.3 | c.325G>A | p.Gly109Ser | missense_variant | 1/6 | ENST00000649141.2 | NP_001020471.3 | |
RAB12 | XR_001753165.2 | n.328G>A | non_coding_transcript_exon_variant | 1/4 | ||||
RAB12 | XR_001753166.2 | n.328G>A | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB12 | ENST00000649141.2 | c.325G>A | p.Gly109Ser | missense_variant | 1/6 | NM_001025300.3 | ENSP00000497886.1 |
Frequencies
GnomAD3 genomes AF: 0.000680 AC: 102AN: 149900Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000465 AC: 52AN: 1118306Hom.: 0 Cov.: 30 AF XY: 0.0000355 AC XY: 19AN XY: 535698
GnomAD4 genome AF: 0.000687 AC: 103AN: 150006Hom.: 0 Cov.: 32 AF XY: 0.000723 AC XY: 53AN XY: 73262
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.37G>A (p.G13S) alteration is located in exon 1 (coding exon 1) of the RAB12 gene. This alteration results from a G to A substitution at nucleotide position 37, causing the glycine (G) at amino acid position 13 to be replaced by a serine (S). 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