rs77706750
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032603.5(LOXL3):c.1124G>A(p.Arg375His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0189 in 1,613,852 control chromosomes in the GnomAD database, including 373 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R375C) has been classified as Benign.
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 | UniProt |
---|---|---|---|---|---|---|---|
LOXL3 | NM_032603.5 | c.1124G>A | p.Arg375His | missense_variant | 7/14 | ENST00000264094.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXL3 | ENST00000264094.8 | c.1124G>A | p.Arg375His | missense_variant | 7/14 | 1 | NM_032603.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0146 AC: 2224AN: 152120Hom.: 24 Cov.: 32
GnomAD3 exomes AF: 0.0147 AC: 3687AN: 251176Hom.: 40 AF XY: 0.0153 AC XY: 2079AN XY: 135772
GnomAD4 exome AF: 0.0194 AC: 28340AN: 1461614Hom.: 349 Cov.: 32 AF XY: 0.0192 AC XY: 13969AN XY: 727128
GnomAD4 genome ? AF: 0.0146 AC: 2221AN: 152238Hom.: 24 Cov.: 32 AF XY: 0.0138 AC XY: 1026AN XY: 74416
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at