chr20-64083831-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001353425.2(LKAAEAR1):āc.389A>Gā(p.Tyr130Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000122 in 1,234,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001353425.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LKAAEAR1 | NM_001353425.2 | c.389A>G | p.Tyr130Cys | missense_variant | 1/3 | ENST00000302096.5 | NP_001340354.1 | |
OPRL1 | NM_182647.4 | c.-185+3479T>C | intron_variant | ENST00000336866.7 | NP_872588.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LKAAEAR1 | ENST00000302096.5 | c.389A>G | p.Tyr130Cys | missense_variant | 1/3 | 2 | NM_001353425.2 | ENSP00000302763.4 | ||
OPRL1 | ENST00000336866.7 | c.-185+3479T>C | intron_variant | 5 | NM_182647.4 | ENSP00000336843.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.0000122 AC: 15AN: 1234120Hom.: 0 Cov.: 35 AF XY: 0.0000133 AC XY: 8AN XY: 600528
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 01, 2024 | The c.389A>G (p.Y130C) alteration is located in exon 1 (coding exon 1) of the LKAAEAR1 gene. This alteration results from a A to G substitution at nucleotide position 389, causing the tyrosine (Y) at amino acid position 130 to be replaced by a cysteine (C). 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