13-26214641-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005977.4(RNF6):c.1241G>A(p.Arg414Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000204 in 1,614,150 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R414P) has been classified as Uncertain significance.
Frequency
Consequence
NM_005977.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF6 | NM_005977.4 | c.1241G>A | p.Arg414Gln | missense_variant | 5/5 | ENST00000381588.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF6 | ENST00000381588.9 | c.1241G>A | p.Arg414Gln | missense_variant | 5/5 | 1 | NM_005977.4 | P1 | |
RNF6 | ENST00000346166.7 | c.1241G>A | p.Arg414Gln | missense_variant | 5/5 | 1 | P1 | ||
RNF6 | ENST00000381570.7 | c.1241G>A | p.Arg414Gln | missense_variant | 5/5 | 1 | P1 | ||
RNF6 | ENST00000468480.5 | n.768+833G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251410Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135876
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461864Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 727238
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.1241G>A (p.R414Q) alteration is located in exon 5 (coding exon 3) of the RNF6 gene. This alteration results from a G to A substitution at nucleotide position 1241, causing the arginine (R) at amino acid position 414 to be replaced by a glutamine (Q). 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