18-46477516-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001384474.1(LOXHD1):c.6778C>T(p.Arg2260Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000413 in 1,550,882 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001384474.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOXHD1 | NM_001384474.1 | c.6778C>T | p.Arg2260Trp | missense_variant | Exon 41 of 41 | ENST00000642948.1 | NP_001371403.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.6778C>T | p.Arg2260Trp | missense_variant | Exon 41 of 41 | NM_001384474.1 | ENSP00000496347.1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000457 AC: 7AN: 153144Hom.: 0 AF XY: 0.0000246 AC XY: 2AN XY: 81450
GnomAD4 exome AF: 0.0000300 AC: 42AN: 1398564Hom.: 0 Cov.: 31 AF XY: 0.0000333 AC XY: 23AN XY: 689792
GnomAD4 genome AF: 0.000144 AC: 22AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74486
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.6592C>T (p.R2198W) alteration is located in exon 40 (coding exon 40) of the LOXHD1 gene. This alteration results from a C to T substitution at nucleotide position 6592, causing the arginine (R) at amino acid position 2198 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at