chr11-17494336-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_153676.4(USH1C):c.2696G>T(p.Arg899Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000328 in 1,607,796 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R899G) has been classified as Uncertain significance.
Frequency
Consequence
NM_153676.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH1C | NM_153676.4 | c.2696G>T | p.Arg899Leu | missense_variant | 27/27 | ENST00000005226.12 | |
USH1C | NM_005709.4 | c.*28G>T | 3_prime_UTR_variant | 21/21 | ENST00000318024.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH1C | ENST00000005226.12 | c.2696G>T | p.Arg899Leu | missense_variant | 27/27 | 5 | NM_153676.4 | ||
USH1C | ENST00000318024.9 | c.*28G>T | 3_prime_UTR_variant | 21/21 | 1 | NM_005709.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152210Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.000125 AC: 30AN: 239586Hom.: 0 AF XY: 0.000170 AC XY: 22AN XY: 129526
GnomAD4 exome AF: 0.000345 AC: 502AN: 1455586Hom.: 1 Cov.: 34 AF XY: 0.000343 AC XY: 248AN XY: 723290
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152210Hom.: 1 Cov.: 34 AF XY: 0.000148 AC XY: 11AN XY: 74356
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 14, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at