12-113191465-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032848.3(RITA1):c.458C>T(p.Ser153Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000299 in 1,604,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RITA1 | NM_032848.3 | c.458C>T | p.Ser153Leu | missense_variant | Exon 4 of 4 | ENST00000548278.2 | NP_116237.1 | |
RITA1 | NM_001286215.2 | c.530C>T | p.Ser177Leu | missense_variant | Exon 3 of 3 | NP_001273144.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RITA1 | ENST00000548278.2 | c.458C>T | p.Ser153Leu | missense_variant | Exon 4 of 4 | 1 | NM_032848.3 | ENSP00000449841.1 | ||
RITA1 | ENST00000552495.1 | c.530C>T | p.Ser177Leu | missense_variant | Exon 3 of 3 | 2 | ENSP00000448680.1 | |||
RITA1 | ENST00000549621.5 | c.458C>T | p.Ser153Leu | missense_variant | Exon 4 of 4 | 2 | ENSP00000448289.1 | |||
ENSG00000257286 | ENST00000552525.1 | n.69+628G>A | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000285 AC: 7AN: 245666Hom.: 0 AF XY: 0.0000301 AC XY: 4AN XY: 133078
GnomAD4 exome AF: 0.0000282 AC: 41AN: 1451916Hom.: 0 Cov.: 31 AF XY: 0.0000264 AC XY: 19AN XY: 720372
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.458C>T (p.S153L) alteration is located in exon 4 (coding exon 2) of the RITA1 gene. This alteration results from a C to T substitution at nucleotide position 458, causing the serine (S) at amino acid position 153 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