1-219179217-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138794.5(LYPLAL1):āc.162A>Gā(p.Ile54Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,612,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_138794.5 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 |
---|---|---|---|---|---|---|---|---|
LYPLAL1 | NM_138794.5 | c.162A>G | p.Ile54Met | missense_variant | 2/5 | ENST00000366928.10 | NP_620149.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LYPLAL1 | ENST00000366928.10 | c.162A>G | p.Ile54Met | missense_variant | 2/5 | 1 | NM_138794.5 | ENSP00000355895 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000840 AC: 21AN: 250062Hom.: 0 AF XY: 0.0000887 AC XY: 12AN XY: 135266
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1459846Hom.: 0 Cov.: 29 AF XY: 0.0000592 AC XY: 43AN XY: 726346
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.162A>G (p.I54M) alteration is located in exon 2 (coding exon 2) of the LYPLAL1 gene. This alteration results from a A to G substitution at nucleotide position 162, causing the isoleucine (I) at amino acid position 54 to be replaced by a methionine (M). 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