14-64948504-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198686.3(RAB15):c.620G>T(p.Arg207Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000243 in 1,606,464 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198686.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB15 | ENST00000533601.7 | c.489G>T | p.Thr163Thr | synonymous_variant | Exon 7 of 7 | 1 | NM_001308154.2 | ENSP00000434103.3 | ||
CHURC1-FNTB | ENST00000549987.1 | c.246+22424C>A | intron_variant | Intron 3 of 13 | 2 | ENSP00000447121.2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000288 AC: 7AN: 242744Hom.: 0 AF XY: 0.0000305 AC XY: 4AN XY: 131150
GnomAD4 exome AF: 0.0000254 AC: 37AN: 1454286Hom.: 0 Cov.: 31 AF XY: 0.0000221 AC XY: 16AN XY: 723058
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.620G>T (p.R207L) alteration is located in exon 7 (coding exon 7) of the RAB15 gene. This alteration results from a G to T substitution at nucleotide position 620, causing the arginine (R) at amino acid position 207 to be replaced by a leucine (L). 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