chr5-1470866-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024830.5(LPCAT1):c.1238G>A(p.Arg413Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000212 in 1,613,500 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 (★). Synonymous variant affecting the same amino acid position (i.e. R413R) has been classified as Benign.
Frequency
Consequence
NM_024830.5 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 | UniProt |
---|---|---|---|---|---|---|---|
LPCAT1 | NM_024830.5 | c.1238G>A | p.Arg413Gln | missense_variant | 12/14 | ENST00000283415.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPCAT1 | ENST00000283415.4 | c.1238G>A | p.Arg413Gln | missense_variant | 12/14 | 1 | NM_024830.5 | P1 | |
LPCAT1 | ENST00000475622.5 | c.1238G>A | p.Arg413Gln | missense_variant, NMD_transcript_variant | 12/17 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250530Hom.: 0 AF XY: 0.0000959 AC XY: 13AN XY: 135584
GnomAD4 exome AF: 0.000220 AC: 322AN: 1461300Hom.: 0 Cov.: 32 AF XY: 0.000206 AC XY: 150AN XY: 726966
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 19, 2023 | The c.1238G>A (p.R413Q) alteration is located in exon 12 (coding exon 12) of the LPCAT1 gene. This alteration results from a G to A substitution at nucleotide position 1238, causing the arginine (R) at amino acid position 413 to be replaced by a glutamine (Q). 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