16-67942417-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000229.2(LCAT):c.694T>A(p.Ser232Thr) variant causes a missense change. The variant allele was found at a frequency of 0.026 in 1,613,908 control chromosomes in the GnomAD database, including 650 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000229.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LCAT | NM_000229.2 | c.694T>A | p.Ser232Thr | missense_variant | Exon 5 of 6 | ENST00000264005.10 | NP_000220.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0173 AC: 2628AN: 152118Hom.: 31 Cov.: 32
GnomAD3 exomes AF: 0.0175 AC: 4389AN: 251330Hom.: 82 AF XY: 0.0175 AC XY: 2381AN XY: 135884
GnomAD4 exome AF: 0.0269 AC: 39307AN: 1461672Hom.: 619 Cov.: 33 AF XY: 0.0261 AC XY: 18971AN XY: 727152
GnomAD4 genome AF: 0.0173 AC: 2627AN: 152236Hom.: 31 Cov.: 32 AF XY: 0.0164 AC XY: 1221AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:3
This variant is associated with the following publications: (PMID: 22090275, 24503134) -
- -
- -
LCAT deficiency Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
LCAT-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Norum disease;C0342895:Fish-eye disease Benign:1
- -
Cardiovascular phenotype Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at