12-96006401-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000895.3(LTA4H):c.1443A>T(p.Glu481Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00424 in 1,599,542 control chromosomes in the GnomAD database, including 233 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E481K) has been classified as Uncertain significance.
Frequency
Consequence
NM_000895.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LTA4H | NM_000895.3 | c.1443A>T | p.Glu481Asp | missense_variant | 16/19 | ENST00000228740.7 | |
LOC102723340 | XR_945236.4 | n.741-3560T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTA4H | ENST00000228740.7 | c.1443A>T | p.Glu481Asp | missense_variant | 16/19 | 1 | NM_000895.3 | P1 | |
ENST00000551849.2 | n.342-3560T>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0220 AC: 3353AN: 152186Hom.: 120 Cov.: 32
GnomAD3 exomes AF: 0.00586 AC: 1459AN: 248866Hom.: 32 AF XY: 0.00415 AC XY: 558AN XY: 134530
GnomAD4 exome AF: 0.00237 AC: 3424AN: 1447238Hom.: 111 Cov.: 26 AF XY: 0.00199 AC XY: 1431AN XY: 720524
GnomAD4 genome ? AF: 0.0221 AC: 3364AN: 152304Hom.: 122 Cov.: 32 AF XY: 0.0206 AC XY: 1535AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at