rs950309128
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001353425.2(LKAAEAR1):c.424A>T(p.Ile142Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000634 in 1,418,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001353425.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LKAAEAR1 | ENST00000302096.5 | c.424A>T | p.Ile142Phe | missense_variant | Exon 2 of 3 | 2 | NM_001353425.2 | ENSP00000302763.4 | ||
OPRL1 | ENST00000336866.7 | c.-185+3332T>A | intron_variant | Intron 1 of 4 | 5 | NM_182647.4 | ENSP00000336843.2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151986Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000553 AC: 7AN: 1266910Hom.: 0 Cov.: 39 AF XY: 0.00000648 AC XY: 4AN XY: 617558
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151986Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74242
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.424A>T (p.I142F) alteration is located in exon 2 (coding exon 2) of the LKAAEAR1 gene. This alteration results from a A to T substitution at nucleotide position 424, causing the isoleucine (I) at amino acid position 142 to be replaced by a phenylalanine (F). 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