5-122070068-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM1BS2
The NM_002317.7(LOX):c.1232G>A(p.Gly411Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,611,030 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G411A) has been classified as Uncertain significance.
Frequency
Consequence
NM_002317.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOX | NM_002317.7 | c.1232G>A | p.Gly411Asp | missense_variant | 6/7 | ENST00000231004.5 | |
LOX | NM_001178102.2 | c.542G>A | p.Gly181Asp | missense_variant | 5/6 | ||
LOX | NM_001317073.1 | c.341G>A | p.Gly114Asp | missense_variant | 5/6 | ||
SRFBP1 | XM_017009111.3 | c.1106-5247C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOX | ENST00000231004.5 | c.1232G>A | p.Gly411Asp | missense_variant | 6/7 | 1 | NM_002317.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152048Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1458864Hom.: 0 Cov.: 30 AF XY: 0.0000220 AC XY: 16AN XY: 725962
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74400
ClinVar
Submissions by phenotype
Aortic aneurysm, familial thoracic 10 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 29, 2023 | The LOX c.1232G>A; p.Gly411Asp variant (rs186028768), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 1215724). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.178). Due to limited information, the clinical significance of this variant is uncertain at this time. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 10, 2020 | Has not been previously published as pathogenic or benign to our knowledge; Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at