rs749182319
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_001384474.1(LOXHD1):c.5514G>A(p.Glu1838=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,550,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000085 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
LOXHD1
NM_001384474.1 synonymous
NM_001384474.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00100
Genes affected
LOXHD1 (HGNC:26521): (lipoxygenase homology PLAT domains 1) This gene encodes a highly conserved protein consisting entirely of PLAT (polycystin/lipoxygenase/alpha-toxin) domains, thought to be involved in targeting proteins to the plasma membrane. Studies in mice show that this gene is expressed in the mechanosensory hair cells in the inner ear, and mutations in this gene lead to auditory defects, indicating that this gene is essential for normal hair cell function. Screening of human families segregating deafness identified a mutation in this gene which causes DFNB77, a progressive form of autosomal-recessive nonsyndromic hearing loss (ARNSHL). Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 18-46509701-C-T is Benign according to our data. Variant chr18-46509701-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 282748.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=2}.
BP7
Synonymous conserved (PhyloP=0.001 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOXHD1 | NM_001384474.1 | c.5514G>A | p.Glu1838= | synonymous_variant | 35/41 | ENST00000642948.1 | NP_001371403.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.5514G>A | p.Glu1838= | synonymous_variant | 35/41 | NM_001384474.1 | ENSP00000496347 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152184Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000145 AC: 23AN: 158360Hom.: 0 AF XY: 0.000216 AC XY: 18AN XY: 83440
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GnomAD4 exome AF: 0.000114 AC: 159AN: 1398526Hom.: 0 Cov.: 31 AF XY: 0.000139 AC XY: 96AN XY: 689856
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GnomAD4 genome AF: 0.0000854 AC: 13AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74344
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:3Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 14, 2015 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 22, 2017 | Variant classified as Uncertain Significance - Favor Benign. The p.Glu1776Glu v ariant in LOXHD1 has not been previously reported in individuals with hearing lo ss, but has been identified in 5/24794 Latino chromosomes by the Genome Aggregat ion Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs749182319). Alth ough this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. It has also been reported in ClinVar (Variation ID: 282748). The variant does not alter an amino acid residue and is not located within the splice consensus sequence; however, this information is n ot sufficient to rule out an impact to splicing or expression of the gene. In su mmary, while the clinical significance of the p.Glu1776Glu variant is uncertain, these data suggest that it is more likely to be benign. ACMG/AMP Criteria appli ed: PM2, BP7. - |
Autosomal recessive nonsyndromic hearing loss 77 Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 24, 2020 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
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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