rs142801489
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The ENST00000318024.9(USH1C):c.1587C>T(p.Gly529=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,613,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G529G) has been classified as Likely benign.
Frequency
Consequence
ENST00000318024.9 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USH1C | NM_153676.4 | c.2487C>T | p.Gly829= | synonymous_variant | 24/27 | ENST00000005226.12 | NP_710142.1 | |
USH1C | NM_005709.4 | c.1587C>T | p.Gly529= | synonymous_variant | 19/21 | ENST00000318024.9 | NP_005700.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USH1C | ENST00000005226.12 | c.2487C>T | p.Gly829= | synonymous_variant | 24/27 | 5 | NM_153676.4 | ENSP00000005226 | ||
USH1C | ENST00000318024.9 | c.1587C>T | p.Gly529= | synonymous_variant | 19/21 | 1 | NM_005709.4 | ENSP00000317018 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000155 AC: 39AN: 251284Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135800
GnomAD4 exome AF: 0.000112 AC: 163AN: 1461476Hom.: 0 Cov.: 30 AF XY: 0.0000949 AC XY: 69AN XY: 727082
GnomAD4 genome AF: 0.000309 AC: 47AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 13, 2020 | See Variant Classification Assertion Criteria. - |
Usher syndrome type 1C;C1865870:Autosomal recessive nonsyndromic hearing loss 18A Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Mar 07, 2018 | - - |
Usher syndrome type 1C Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at