chr12-96013817-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The ENST00000228740.7(LTA4H):āc.1241A>Cā(p.Lys414Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00014 in 1,575,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000228740.7 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LTA4H | NM_000895.3 | c.1241A>C | p.Lys414Thr | missense_variant | 13/19 | ENST00000228740.7 | NP_000886.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LTA4H | ENST00000228740.7 | c.1241A>C | p.Lys414Thr | missense_variant | 13/19 | 1 | NM_000895.3 | ENSP00000228740.2 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000502 AC: 12AN: 239050Hom.: 0 AF XY: 0.0000616 AC XY: 8AN XY: 129768
GnomAD4 exome AF: 0.000147 AC: 209AN: 1423628Hom.: 0 Cov.: 24 AF XY: 0.000132 AC XY: 94AN XY: 710382
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.1241A>C (p.K414T) alteration is located in exon 13 (coding exon 13) of the LTA4H gene. This alteration results from a A to C substitution at nucleotide position 1241, causing the lysine (K) at amino acid position 414 to be replaced by a threonine (T). 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