chr16-67944009-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000229.2(LCAT):c.93C>T(p.Leu31=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000388 in 1,548,272 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L31L) has been classified as Likely benign.
Frequency
Consequence
NM_000229.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCAT | NM_000229.2 | c.93C>T | p.Leu31= | synonymous_variant | 1/6 | ENST00000264005.10 | |
SLC12A4 | NM_005072.5 | c.*831C>T | 3_prime_UTR_variant | 24/24 | ENST00000316341.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCAT | ENST00000264005.10 | c.93C>T | p.Leu31= | synonymous_variant | 1/6 | 1 | NM_000229.2 | P1 | |
SLC12A4 | ENST00000316341.8 | c.*831C>T | 3_prime_UTR_variant | 24/24 | 1 | NM_005072.5 | P1 | ||
LCAT | ENST00000575467.5 | c.93C>T | p.Leu31= | synonymous_variant, NMD_transcript_variant | 1/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000130 AC: 2AN: 153552Hom.: 0 AF XY: 0.0000123 AC XY: 1AN XY: 81006
GnomAD4 exome AF: 0.00000215 AC: 3AN: 1396116Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 688418
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74326
ClinVar
Submissions by phenotype
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 04, 2022 | This alteration is classified as likely 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