rs114974101
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001384474.1(LOXHD1):c.5868C>T(p.His1956His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,551,634 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001384474.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOXHD1 | NM_001384474.1 | c.5868C>T | p.His1956His | synonymous_variant | Exon 37 of 41 | ENST00000642948.1 | NP_001371403.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.5868C>T | p.His1956His | synonymous_variant | Exon 37 of 41 | NM_001384474.1 | ENSP00000496347.1 |
Frequencies
GnomAD3 genomes AF: 0.00521 AC: 792AN: 152112Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00111 AC: 173AN: 156300Hom.: 2 AF XY: 0.000833 AC XY: 69AN XY: 82824
GnomAD4 exome AF: 0.000569 AC: 796AN: 1399404Hom.: 6 Cov.: 31 AF XY: 0.000542 AC XY: 374AN XY: 690196
GnomAD4 genome AF: 0.00522 AC: 795AN: 152230Hom.: 11 Cov.: 32 AF XY: 0.00474 AC XY: 353AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
His1894His in Exon 36 of LOXHD1: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wit hin the splice consensus sequence, and has been identified in 2.1% (15/702) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs114974101). -
Autosomal recessive nonsyndromic hearing loss 77 Benign:1
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LOXHD1-related disorder Benign:1
This variant is classified as 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