1-185087566-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007212.4(RNF2):c.13G>T(p.Val5Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,736 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V5M) has been classified as Uncertain significance.
Frequency
Consequence
NM_007212.4 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 |
---|---|---|---|---|---|---|---|
RNF2 | NM_007212.4 | c.13G>T | p.Val5Leu | missense_variant | 2/7 | ENST00000367510.8 | |
RNF2 | XM_011509851.4 | c.13G>T | p.Val5Leu | missense_variant | 2/7 | ||
RNF2 | XM_011509852.3 | c.13G>T | p.Val5Leu | missense_variant | 2/7 | ||
RNF2 | XM_005245413.4 | c.-149G>T | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF2 | ENST00000367510.8 | c.13G>T | p.Val5Leu | missense_variant | 2/7 | 1 | NM_007212.4 | P1 | |
RNF2 | ENST00000367509.8 | c.13G>T | p.Val5Leu | missense_variant | 2/6 | 2 | |||
RNF2 | ENST00000453650.2 | c.13G>T | p.Val5Leu | missense_variant | 2/5 | 5 | |||
RNF2 | ENST00000498201.1 | n.129G>T | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461736Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727194
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2023 | The c.13G>T (p.V5L) alteration is located in exon 2 (coding exon 1) of the RNF2 gene. This alteration results from a G to T substitution at nucleotide position 13, causing the valine (V) at amino acid position 5 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