18-46534398-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001384474.1(LOXHD1):c.4149G>A(p.Thr1383=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000973 in 1,551,502 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T1383T) has been classified as Likely benign.
Frequency
Consequence
NM_001384474.1 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOXHD1 | NM_001384474.1 | c.4149G>A | p.Thr1383= | synonymous_variant | 27/41 | ENST00000642948.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.4149G>A | p.Thr1383= | synonymous_variant | 27/41 | NM_001384474.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000440 AC: 7AN: 158988Hom.: 0 AF XY: 0.0000597 AC XY: 5AN XY: 83688
GnomAD4 exome AF: 0.000101 AC: 142AN: 1399444Hom.: 0 Cov.: 30 AF XY: 0.000101 AC XY: 70AN XY: 690218
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74272
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | Thr1383Thr in Exon 27 of LOXHD1: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 1/2532 European Ame rican chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS). - |
Autosomal recessive nonsyndromic hearing loss 77 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Counsyl | Apr 26, 2018 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | LOXHD1: BP4, BP7 - |
LOXHD1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 25, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at