rs1013013
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_173477.5(USH1G):c.*1303C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,234 control chromosomes in the GnomAD database, including 3,313 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.21 ( 3308 hom., cov: 33)
Exomes 𝑓: 0.25 ( 5 hom. )
Consequence
USH1G
NM_173477.5 3_prime_UTR
NM_173477.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.24
Genes affected
USH1G (HGNC:16356): (USH1 protein network component sans) This gene encodes a protein that contains three ankyrin domains, a class I PDZ-binding motif and a sterile alpha motif. The encoded protein interacts with harmonin, which is associated with Usher syndrome type 1C. This protein plays a role in the development and maintenance of the auditory and visual systems and functions in the cohesion of hair bundles formed by inner ear sensory cells. Mutations in this gene are associated with Usher syndrome type 1G (USH1G). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 17-74916770-G-A is Benign according to our data. Variant chr17-74916770-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 325034.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH1G | NM_173477.5 | c.*1303C>T | 3_prime_UTR_variant | 3/3 | ENST00000614341.5 | ||
USH1G | NM_001282489.3 | c.*1303C>T | 3_prime_UTR_variant | 3/3 | |||
USH1G | XM_011524296.2 | c.*1303C>T | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH1G | ENST00000614341.5 | c.*1303C>T | 3_prime_UTR_variant | 3/3 | 1 | NM_173477.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.207 AC: 31403AN: 151986Hom.: 3311 Cov.: 33
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GnomAD4 exome AF: 0.254 AC: 33AN: 130Hom.: 5 Cov.: 0 AF XY: 0.233 AC XY: 20AN XY: 86
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GnomAD4 genome ? AF: 0.206 AC: 31402AN: 152104Hom.: 3308 Cov.: 33 AF XY: 0.210 AC XY: 15593AN XY: 74352
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Usher syndrome type 1G Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at