chr5-1474576-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024830.5(LPCAT1):c.1009C>G(p.Leu337Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,642 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L337F) has been classified as Uncertain significance.
Frequency
Consequence
NM_024830.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LPCAT1 | NM_024830.5 | c.1009C>G | p.Leu337Val | missense_variant | 10/14 | ENST00000283415.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPCAT1 | ENST00000283415.4 | c.1009C>G | p.Leu337Val | missense_variant | 10/14 | 1 | NM_024830.5 | P1 | |
LPCAT1 | ENST00000475622.5 | c.1009C>G | p.Leu337Val | missense_variant, NMD_transcript_variant | 10/17 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250796Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135724
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461642Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727104
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.1009C>G (p.L337V) alteration is located in exon 10 (coding exon 10) of the LPCAT1 gene. This alteration results from a C to G substitution at nucleotide position 1009, causing the leucine (L) at amino acid position 337 to be replaced by a valine (V). 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