rs757572697
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153676.4(USH1C):c.2695C>T(p.Arg899Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,607,562 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R899L) has been classified as Likely benign.
Frequency
Consequence
NM_153676.4 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 |
---|---|---|---|---|---|---|---|---|
USH1C | NM_153676.4 | c.2695C>T | p.Arg899Cys | missense_variant | Exon 27 of 27 | ENST00000005226.12 | NP_710142.1 | |
USH1C | NM_005709.4 | c.*27C>T | 3_prime_UTR_variant | Exon 21 of 21 | ENST00000318024.9 | NP_005700.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USH1C | ENST00000005226.12 | c.2695C>T | p.Arg899Cys | missense_variant | Exon 27 of 27 | 5 | NM_153676.4 | ENSP00000005226.7 | ||
USH1C | ENST00000318024 | c.*27C>T | 3_prime_UTR_variant | Exon 21 of 21 | 1 | NM_005709.4 | ENSP00000317018.4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000293 AC: 7AN: 238758Hom.: 0 AF XY: 0.0000388 AC XY: 5AN XY: 129018
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1455328Hom.: 0 Cov.: 34 AF XY: 0.0000138 AC XY: 10AN XY: 723108
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at