chr16-67943957-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000229.2(LCAT):c.145G>A(p.Val49Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000582 in 1,546,268 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 (★★).
Frequency
Consequence
NM_000229.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LCAT | NM_000229.2 | c.145G>A | p.Val49Ile | missense_variant | Exon 1 of 6 | ENST00000264005.10 | NP_000220.1 | |
SLC12A4 | NM_005072.5 | c.*883G>A | 3_prime_UTR_variant | Exon 24 of 24 | ENST00000316341.8 | NP_005063.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LCAT | ENST00000264005.10 | c.145G>A | p.Val49Ile | missense_variant | Exon 1 of 6 | 1 | NM_000229.2 | ENSP00000264005.5 | ||
SLC12A4 | ENST00000316341 | c.*883G>A | 3_prime_UTR_variant | Exon 24 of 24 | 1 | NM_005072.5 | ENSP00000318557.3 | |||
LCAT | ENST00000575467.5 | n.145G>A | non_coding_transcript_exon_variant | Exon 1 of 6 | 5 | ENSP00000460653.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152072Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000502 AC: 7AN: 1394196Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 687294
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152072Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74276
ClinVar
Submissions by phenotype
Norum disease;C0342895:Fish-eye disease Uncertain:1
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Cardiovascular phenotype Uncertain:1
The p.V49I variant (also known as c.145G>A), located in coding exon 1 of the LCAT gene, results from a G to A substitution at nucleotide position 145. The valine at codon 49 is replaced by isoleucine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at