chr16-28984913-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001014989.2(LAT):c.52G>T(p.Ala18Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000429 in 1,546,618 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001014989.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000394 AC: 60AN: 152156Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00367 AC: 514AN: 140060Hom.: 11 AF XY: 0.00256 AC XY: 193AN XY: 75444
GnomAD4 exome AF: 0.000432 AC: 603AN: 1394344Hom.: 14 Cov.: 32 AF XY: 0.000350 AC XY: 241AN XY: 687794
GnomAD4 genome AF: 0.000394 AC: 60AN: 152274Hom.: 1 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74448
ClinVar
Submissions by phenotype
LAT-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 16, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2024 | LAT: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at