chr2-86612244-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005667.4(RNF103):c.397G>C(p.Gly133Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,613,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005667.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF103 | NM_005667.4 | c.397G>C | p.Gly133Arg | missense_variant | 3/4 | ENST00000237455.5 | |
RNF103-CHMP3 | NM_001198954.1 | c.132+8086G>C | intron_variant | ||||
CHMP3-AS1 | NR_183900.1 | n.254-4932C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF103 | ENST00000237455.5 | c.397G>C | p.Gly133Arg | missense_variant | 3/4 | 1 | NM_005667.4 | P1 | |
CHMP3-AS1 | ENST00000439077.1 | n.249-4932C>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152046Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250602Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135492
GnomAD4 exome AF: 0.000138 AC: 202AN: 1461010Hom.: 0 Cov.: 30 AF XY: 0.000133 AC XY: 97AN XY: 726818
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152046Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74244
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.397G>C (p.G133R) alteration is located in exon 3 (coding exon 3) of the RNF103 gene. This alteration results from a G to C substitution at nucleotide position 397, causing the glycine (G) at amino acid position 133 to be replaced by an arginine (R). 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