rs1553257690
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_206933.4(USH2A):c.11500T>A(p.Leu3834Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,272 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 Uncertain significance (★).
Frequency
Consequence
NM_206933.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.11500T>A | p.Leu3834Met | missense_variant | Exon 59 of 72 | 1 | NM_206933.4 | ENSP00000305941.3 | ||
USH2A | ENST00000674083.1 | c.11500T>A | p.Leu3834Met | missense_variant | Exon 59 of 73 | ENSP00000501296.1 |
Frequencies
GnomAD3 genomes Cov.: 27
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461272Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726962
GnomAD4 genome Cov.: 27
ClinVar
Submissions by phenotype
not specified Uncertain:1
The p.Leu3834Met variant in USH2A has not been previously reported in individual s with hearing loss or in large population studies. Computational prediction too ls and conservation analysis suggest that the p.Leu3834Met variant may impact th e protein, though this information is not predictive enough to determine pathoge nicity. In summary, the clinical significance of the p.Leu3834Met variant is unc ertain -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at