rs17010021
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032603.5(LOXL3):c.1843A>T(p.Ile615Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 1,614,118 control chromosomes in the GnomAD database, including 5,524 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_032603.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOXL3 | NM_032603.5 | c.1843A>T | p.Ile615Phe | missense_variant | 11/14 | ENST00000264094.8 | NP_115992.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LOXL3 | ENST00000264094.8 | c.1843A>T | p.Ile615Phe | missense_variant | 11/14 | 1 | NM_032603.5 | ENSP00000264094.3 |
Frequencies
GnomAD3 genomes AF: 0.0545 AC: 8299AN: 152164Hom.: 538 Cov.: 33
GnomAD3 exomes AF: 0.0825 AC: 20741AN: 251482Hom.: 1821 AF XY: 0.0821 AC XY: 11154AN XY: 135910
GnomAD4 exome AF: 0.0547 AC: 80007AN: 1461836Hom.: 4986 Cov.: 33 AF XY: 0.0562 AC XY: 40891AN XY: 727218
GnomAD4 genome AF: 0.0545 AC: 8301AN: 152282Hom.: 538 Cov.: 33 AF XY: 0.0584 AC XY: 4346AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 16, 2019 | This variant is associated with the following publications: (PMID: 29802726) - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at