rs78803776
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005576.4(LOXL1):āc.475T>Gā(p.Ser159Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00821 in 1,601,216 control chromosomes in the GnomAD database, including 913 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_005576.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOXL1 | NM_005576.4 | c.475T>G | p.Ser159Ala | missense_variant | 1/7 | ENST00000261921.8 | |
LOXL1-AS1 | NR_040069.1 | n.184+807A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LOXL1 | ENST00000261921.8 | c.475T>G | p.Ser159Ala | missense_variant | 1/7 | 1 | NM_005576.4 | P1 | |
LOXL1-AS1 | ENST00000685373.1 | n.198+519A>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0451 AC: 6861AN: 152084Hom.: 508 Cov.: 33
GnomAD3 exomes AF: 0.0106 AC: 2413AN: 227168Hom.: 175 AF XY: 0.00763 AC XY: 956AN XY: 125364
GnomAD4 exome AF: 0.00433 AC: 6269AN: 1449024Hom.: 404 Cov.: 36 AF XY: 0.00365 AC XY: 2632AN XY: 721184
GnomAD4 genome ? AF: 0.0451 AC: 6870AN: 152192Hom.: 509 Cov.: 33 AF XY: 0.0431 AC XY: 3209AN XY: 74418
ClinVar
Submissions by phenotype
LOXL1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 24, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at