chr15-73927471-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005576.4(LOXL1):c.688C>A(p.Pro230Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,450,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_005576.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOXL1 | NM_005576.4 | c.688C>A | p.Pro230Thr | missense_variant | 1/7 | ENST00000261921.8 | NP_005567.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LOXL1 | ENST00000261921.8 | c.688C>A | p.Pro230Thr | missense_variant | 1/7 | 1 | NM_005576.4 | ENSP00000261921.7 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152056Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000178 AC: 1AN: 56244Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 31814
GnomAD4 exome AF: 0.00000385 AC: 5AN: 1298550Hom.: 0 Cov.: 36 AF XY: 0.00000157 AC XY: 1AN XY: 637126
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152056Hom.: 0 Cov.: 33 AF XY: 0.0000539 AC XY: 4AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 26, 2024 | The c.688C>A (p.P230T) alteration is located in exon 1 (coding exon 1) of the LOXL1 gene. This alteration results from a C to A substitution at nucleotide position 688, causing the proline (P) at amino acid position 230 to be replaced by a threonine (T). 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