11-17509638-C-G
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_153676.4(USH1C):āc.1731G>Cā(p.Pro577=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P577P) has been classified as Likely benign.
Frequency
Genomes: š 0.0 ( 0 hom., cov: 18)
Exomes š: 0.0000044 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
USH1C
NM_153676.4 synonymous
NM_153676.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.68
Genes affected
USH1C (HGNC:12597): (USH1 protein network component harmonin) This gene encodes a scaffold protein that functions in the assembly of Usher protein complexes. The protein contains PDZ domains, a coiled-coil region with a bipartite nuclear localization signal and a PEST degradation sequence. Defects in this gene are the cause of Usher syndrome type 1C and non-syndromic sensorineural deafness autosomal recessive type 18. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP7
Synonymous conserved (PhyloP=-5.68 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH1C | NM_153676.4 | c.1731G>C | p.Pro577= | synonymous_variant | 18/27 | ENST00000005226.12 | |
USH1C | NM_005709.4 | c.1285-7658G>C | intron_variant | ENST00000318024.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH1C | ENST00000005226.12 | c.1731G>C | p.Pro577= | synonymous_variant | 18/27 | 5 | NM_153676.4 | ||
USH1C | ENST00000318024.9 | c.1285-7658G>C | intron_variant | 1 | NM_005709.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 69378Hom.: 0 Cov.: 18 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000437 AC: 5AN: 1145198Hom.: 0 Cov.: 40 AF XY: 0.00000356 AC XY: 2AN XY: 562464
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GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 69378Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 32742
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at