5-90118337-TTTTTGTGATGATGTTGTTTTTAGACATTGTATCTCTCTCTCTCTGTCATCCATGCCCTACACTTCAGTTAAAACACATGAGTAGCTAGTACCAAAATGTCCCACATCGTGCTGTACTTCTGTGTTGAAGCTTCTATTACTGTTTTTCAAAATCAAATTTCTTTGGGTCAGGCACAGTGGCTTATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCGGATCACAAGGTCAGGAGTTCAAGACCAACCTGGCCAACATAGTGAAACCCCATCTCTACTAAAAATACAAAAAAATTTGCTGGGCGTGGTGGTGGGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCACGAGAATTGCTTGAACCTAGGGGACGGAGTTTGGAGTGAGCCGAGATCACGCCACTGCACTCCAGCCCGGGCAATGGTGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAGAAATCAAATTTCTTTGGAAATTAACAATTCATTAGGACAGGTTTGATGAAACCTGAAAGAAAGATTTCATGATTTTCTTAGGCAAAAAATTATCTAATGTAATTATATATATTATTAAAGTTAAAGATGATGGGGCTGGGTGGATGTGGGGAAGTAAGGGGAAAGTTGACTTGAATCACCAATGCAGAAGCCACTTTATACAACTATTATGAGCCATGAAATTATTTTTAAAAGCCACATGGAAACTTTTTTATTCTAAATGTATTTTTTCTGAATAATTCTTTCAGAAGCAATCAAGGTAAAAGACTTTGACTTTTGCATAACTATACTATAGGCAGTCACAGTGTATCAGTTTGACCTCACTGCTTTCTGAGCTGACAAGTCTCAGGCATTTGATGAAACCAATATCCACCCATGCCATAGAGTAGAACAATATTTAGACA-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Consequence
Unknown
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.68
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 5-90118337-TTTTTGTGATGATGTTGTTTTTAGACATTGTATCTCTCTCTCTCTGTCATCCATGCCCTACACTTCAGTTAAAACACATGAGTAGCTAGTACCAAAATGTCCCACATCGTGCTGTACTTCTGTGTTGAAGCTTCTATTACTGTTTTTCAAAATCAAATTTCTTTGGGTCAGGCACAGTGGCTTATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCGGATCACAAGGTCAGGAGTTCAAGACCAACCTGGCCAACATAGTGAAACCCCATCTCTACTAAAAATACAAAAAAATTTGCTGGGCGTGGTGGTGGGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCACGAGAATTGCTTGAACCTAGGGGACGGAGTTTGGAGTGAGCCGAGATCACGCCACTGCACTCCAGCCCGGGCAATGGTGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAGAAATCAAATTTCTTTGGAAATTAACAATTCATTAGGACAGGTTTGATGAAACCTGAAAGAAAGATTTCATGATTTTCTTAGGCAAAAAATTATCTAATGTAATTATATATATTATTAAAGTTAAAGATGATGGGGCTGGGTGGATGTGGGGAAGTAAGGGGAAAGTTGACTTGAATCACCAATGCAGAAGCCACTTTATACAACTATTATGAGCCATGAAATTATTTTTAAAAGCCACATGGAAACTTTTTTATTCTAAATGTATTTTTTCTGAATAATTCTTTCAGAAGCAATCAAGGTAAAAGACTTTGACTTTTGCATAACTATACTATAGGCAGTCACAGTGTATCAGTTTGACCTCACTGCTTTCTGAGCTGACAAGTCTCAGGCATTTGATGAAACCAATATCCACCCATGCCATAGAGTAGAACAATATTTAGACA-T is Pathogenic according to our data. Variant chr5-90118337-TTTTTGTGATGATGTTGTTTTTAGACATTGTATCTCTCTCTCTCTGTCATCCATGCCCTACACTTCAGTTAAAACACATGAGTAGCTAGTACCAAAATGTCCCACATCGTGCTGTACTTCTGTGTTGAAGCTTCTATTACTGTTTTTCAAAATCAAATTTCTTTGGGTCAGGCACAGTGGCTTATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCGGATCACAAGGTCAGGAGTTCAAGACCAACCTGGCCAACATAGTGAAACCCCATCTCTACTAAAAATACAAAAAAATTTGCTGGGCGTGGTGGTGGGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCACGAGAATTGCTTGAACCTAGGGGACGGAGTTTGGAGTGAGCCGAGATCACGCCACTGCACTCCAGCCCGGGCAATGGTGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAGAAATCAAATTTCTTTGGAAATTAACAATTCATTAGGACAGGTTTGATGAAACCTGAAAGAAAGATTTCATGATTTTCTTAGGCAAAAAATTATCTAATGTAATTATATATATTATTAAAGTTAAAGATGATGGGGCTGGGTGGATGTGGGGAAGTAAGGGGAAAGTTGACTTGAATCACCAATGCAGAAGCCACTTTATACAACTATTATGAGCCATGAAATTATTTTTAAAAGCCACATGGAAACTTTTTTATTCTAAATGTATTTTTTCTGAATAATTCTTTCAGAAGCAATCAAGGTAAAAGACTTTGACTTTTGCATAACTATACTATAGGCAGTCACAGTGTATCAGTTTGACCTCACTGCTTTCTGAGCTGACAAGTCTCAGGCATTTGATGAAACCAATATCCACCCATGCCATAGAGTAGAACAATATTTAGACA-T is described in ClinVar as [Pathogenic]. Clinvar id is 2445626.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
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Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Usher syndrome type 2C Pathogenic:1
Pathogenic, criteria provided, single submitter | research | King Laboratory, University of Washington | Feb 28, 2023 | This variant was found in homozygosity in two siblings with Usher Syndrome Type 2, in a study of pediatric hearing loss conducted by the King Laboratory (Carlson RJ et al. JAMA-OtoHNS 2023). These two patients were born to consanguineous parents and have a 1st cousin with a similar hearing loss. This variant is a chromosomal deletion that is predicted to alter splicing. The deletion includes the 5’ end of ADGRV1 exon 76, which is likely to lead to exon skipping, a frameshift in the coding sequence, and early truncation. As of January 2023, this variant has not been reported to ClinVar and is not found on gnomAD. Based on the prediction that this variant leads to a splicing error and a truncated protein, co-segregation with the phenotype in the family, and goodness of fit of genotype to phenotype, we conclude that this variant is pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.