13-26214743-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005977.4(RNF6):āc.1139A>Gā(p.Glu380Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,461,876 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 (ā ).
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.1139A>G | p.Glu380Gly | missense_variant | 5/5 | ENST00000381588.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF6 | ENST00000381588.9 | c.1139A>G | p.Glu380Gly | missense_variant | 5/5 | 1 | NM_005977.4 | P1 | |
RNF6 | ENST00000346166.7 | c.1139A>G | p.Glu380Gly | missense_variant | 5/5 | 1 | P1 | ||
RNF6 | ENST00000381570.7 | c.1139A>G | p.Glu380Gly | missense_variant | 5/5 | 1 | P1 | ||
RNF6 | ENST00000468480.5 | n.768+731A>G | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251454Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135900
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461876Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 727238
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2022 | The c.1139A>G (p.E380G) alteration is located in exon 5 (coding exon 3) of the RNF6 gene. This alteration results from a A to G substitution at nucleotide position 1139, causing the glutamic acid (E) at amino acid position 380 to be replaced by a glycine (G). 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