chr3-49701513-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022064.5(RNF123):c.1300G>A(p.Val434Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,748 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 (★).
Frequency
Consequence
NM_022064.5 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 |
---|---|---|---|---|---|---|---|
RNF123 | NM_022064.5 | c.1300G>A | p.Val434Ile | missense_variant | 16/39 | ENST00000327697.11 | |
RNF123 | NR_135218.2 | n.1386G>A | non_coding_transcript_exon_variant | 16/39 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF123 | ENST00000327697.11 | c.1300G>A | p.Val434Ile | missense_variant | 16/39 | 1 | NM_022064.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251022Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135780
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461436Hom.: 0 Cov.: 33 AF XY: 0.0000179 AC XY: 13AN XY: 727036
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152312Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 28, 2023 | The c.1300G>A (p.V434I) alteration is located in exon 16 (coding exon 15) of the RNF123 gene. This alteration results from a G to A substitution at nucleotide position 1300, causing the valine (V) at amino acid position 434 to be replaced by an isoleucine (I). 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