rs1341364071
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001025.5(RPS23):c.-14G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001025.5 5_prime_UTR_premature_start_codon_gain
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 |
---|---|---|---|---|---|---|---|---|
RPS23 | NM_001025.5 | c.-14G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 4 | ENST00000296674.13 | NP_001016.1 | ||
RPS23 | NM_001025.5 | c.-14G>T | 5_prime_UTR_variant | Exon 1 of 4 | ENST00000296674.13 | NP_001016.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPS23 | ENST00000296674.13 | c.-14G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 4 | 1 | NM_001025.5 | ENSP00000296674.8 | |||
RPS23 | ENST00000296674.13 | c.-14G>T | 5_prime_UTR_variant | Exon 1 of 4 | 1 | NM_001025.5 | ENSP00000296674.8 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1456102Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 723768
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: RPS23 c.-14G>T is located in the untranslated mRNA region upstream of the initiation codon. The frequency data for this variant in gnomAD is considered unreliable, as metrics indicate poor data quality at this position. To our knowledge, no occurrence of c.-14G>T in individuals affected with Brachycephaly, Trichomegaly, And Developmental Delay and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at