rs876657857
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001384474.1(LOXHD1):c.131-11_131-10delTCinsAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001384474.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.131-11_131-10delTCinsAA | intron_variant | Intron 1 of 40 | NM_001384474.1 | ENSP00000496347.1 | ||||
LOXHD1 | ENST00000536736.5 | c.131-11_131-10delTCinsAA | intron_variant | Intron 1 of 39 | 5 | ENSP00000444586.1 | ||||
LOXHD1 | ENST00000441551.6 | c.131-11_131-10delTCinsAA | intron_variant | Intron 1 of 38 | 5 | ENSP00000387621.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.131-11_131-10delinsAA variant in LOXHD1 has not been previously reported i n individuals with hearing loss. Data from large population studies are insuffic ient to assess the frequency of this variant. This variant is located in the 3' splice region. Computational tools do not suggest an impact to splicing. However , this information is not predictive enough to rule out pathogenicity. In summar y, the clinical significance of the c.131-11_131-10delinsAA variant is uncertain . -
not provided Uncertain:1
This sequence change falls in intron 1 of the LOXHD1 gene. It does not directly change the encoded amino acid sequence of the LOXHD1 protein. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This variant has not been reported in the literature in individuals affected with LOXHD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 228812). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at