rs121912598
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_206933.4(USH2A):āc.779T>Gā(p.Leu260Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. L260L) has been classified as Uncertain significance. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_206933.4 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.779T>G | p.Leu260Ter | stop_gained | 4/72 | ENST00000307340.8 | |
USH2A | NM_007123.6 | c.779T>G | p.Leu260Ter | stop_gained | 4/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.779T>G | p.Leu260Ter | stop_gained | 4/72 | 1 | NM_206933.4 | P1 | |
USH2A | ENST00000366942.3 | c.779T>G | p.Leu260Ter | stop_gained | 4/21 | 1 | |||
USH2A | ENST00000674083.1 | c.779T>G | p.Leu260Ter | stop_gained | 4/73 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250978Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135638
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461182Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726902
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Usher syndrome type 2A Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at