rs869312982
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000257700.7(RINT1):āc.1447A>Gā(p.Met483Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,610,494 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M483I) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000257700.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RINT1 | NM_021930.6 | c.1447A>G | p.Met483Val | missense_variant | 10/15 | ENST00000257700.7 | NP_068749.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RINT1 | ENST00000257700.7 | c.1447A>G | p.Met483Val | missense_variant | 10/15 | 1 | NM_021930.6 | ENSP00000257700 | P1 | |
RINT1 | ENST00000474123.1 | n.451A>G | non_coding_transcript_exon_variant | 3/4 | 2 | |||||
RINT1 | ENST00000497979.5 | c.*1052A>G | 3_prime_UTR_variant, NMD_transcript_variant | 10/15 | 5 | ENSP00000420582 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458288Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 725342
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 27, 2015 | In summary, this is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This sequence change replaces methionine with valine at codon 483 of the RINT1 protein (p.Met483Val). The methionine residue is highly conserved and there is a small physicochemical difference between methionine and valine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at