2-129980136-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032144.3(RAB6C):c.21C>A(p.Phe7Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000263 in 152,240 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032144.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAB6C | NM_032144.3 | c.21C>A | p.Phe7Leu | missense_variant | 1/1 | ENST00000410061.4 | NP_115520.2 | |
RAB6C-AS1 | NR_036537.1 | n.223G>T | non_coding_transcript_exon_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB6C | ENST00000410061.4 | c.21C>A | p.Phe7Leu | missense_variant | 1/1 | 6 | NM_032144.3 | ENSP00000387307.2 | ||
RAB6C-AS1 | ENST00000412425.1 | n.217G>T | non_coding_transcript_exon_variant | 2/6 | 1 | |||||
RAB6C-AS1 | ENST00000624615.1 | n.277G>T | non_coding_transcript_exon_variant | 1/1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152124Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000459 AC: 7AN: 152620Hom.: 0 AF XY: 0.0000493 AC XY: 4AN XY: 81058
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000188 AC: 27AN: 1437334Hom.: 0 Cov.: 36 AF XY: 0.0000267 AC XY: 19AN XY: 712772
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152240Hom.: 0 Cov.: 30 AF XY: 0.0000134 AC XY: 1AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 02, 2023 | The c.21C>A (p.F7L) alteration is located in exon 1 (coding exon 1) of the RAB6C gene. This alteration results from a C to A substitution at nucleotide position 21, causing the phenylalanine (F) at amino acid position 7 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