chr18-46485129-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.6072G>A(p.Thr2024=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000774 in 1,549,522 control chromosomes in the GnomAD database, including 1 homozygotes. 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. T2024T) 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.6072G>A | p.Thr2024= | synonymous_variant | 39/41 | ENST00000642948.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXHD1 | ENST00000642948.1 | c.6072G>A | p.Thr2024= | synonymous_variant | 39/41 | NM_001384474.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000667 AC: 1AN: 150034Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000631 AC: 1AN: 158360Hom.: 0 AF XY: 0.0000120 AC XY: 1AN XY: 83544
GnomAD4 exome AF: 0.00000786 AC: 11AN: 1399488Hom.: 1 Cov.: 35 AF XY: 0.00000580 AC XY: 4AN XY: 690234
GnomAD4 genome AF: 0.00000667 AC: 1AN: 150034Hom.: 0 Cov.: 30 AF XY: 0.0000137 AC XY: 1AN XY: 73012
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 | Sep 02, 2017 | p.Thr1962Thr in exon 38 of LOXHD1: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 1/58842 of Euro pean chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broad institute.org/). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at