chr17-74916083-T-C
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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.*1990A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0358 in 128,730 control chromosomes in the GnomAD database, including 205 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.036 ( 205 hom., cov: 26)
Exomes 𝑓: 0.042 ( 0 hom. )
Consequence
USH1G
NM_173477.5 3_prime_UTR
NM_173477.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.112
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=-0.9).
BP6
Variant 17-74916083-T-C is Benign according to our data. Variant chr17-74916083-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 369224.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH1G | NM_173477.5 | c.*1990A>G | 3_prime_UTR_variant | 3/3 | ENST00000614341.5 | ||
USH1G | NM_001282489.3 | c.*1990A>G | 3_prime_UTR_variant | 3/3 | |||
USH1G | XM_011524296.2 | c.*1990A>G | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH1G | ENST00000614341.5 | c.*1990A>G | 3_prime_UTR_variant | 3/3 | 1 | NM_173477.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0356 AC: 4581AN: 128638Hom.: 202 Cov.: 26
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GnomAD4 exome AF: 0.0417 AC: 1AN: 24Hom.: 0 Cov.: 0 AF XY: 0.0833 AC XY: 1AN XY: 12
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GnomAD4 genome AF: 0.0358 AC: 4604AN: 128706Hom.: 205 Cov.: 26 AF XY: 0.0364 AC XY: 2192AN XY: 60182
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Retinitis pigmentosa-deafness syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at