12-113187020-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032848.3(RITA1):c.274C>G(p.Leu92Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000125 in 1,605,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032848.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RITA1 | NM_032848.3 | c.274C>G | p.Leu92Val | missense_variant | Exon 3 of 4 | ENST00000548278.2 | NP_116237.1 | |
RITA1 | NM_001286215.2 | c.346C>G | p.Leu116Val | missense_variant | Exon 2 of 3 | NP_001273144.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152238Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000867 AC: 2AN: 230764Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 125188
GnomAD4 exome AF: 0.00000482 AC: 7AN: 1452818Hom.: 0 Cov.: 31 AF XY: 0.00000416 AC XY: 3AN XY: 721988
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.274C>G (p.L92V) alteration is located in exon 3 (coding exon 1) of the RITA1 gene. This alteration results from a C to G substitution at nucleotide position 274, causing the leucine (L) at amino acid position 92 to be replaced by a valine (V). 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