16-28984905-T-TG
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_001014989.2(LAT):c.52dupG(p.Ala18GlyfsTer8) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000055 in 1,544,818 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_001014989.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151530Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000306 AC: 41AN: 133958Hom.: 0 AF XY: 0.000319 AC XY: 23AN XY: 72134
GnomAD4 exome AF: 0.0000574 AC: 80AN: 1393288Hom.: 0 Cov.: 32 AF XY: 0.0000626 AC XY: 43AN XY: 687292
GnomAD4 genome AF: 0.0000330 AC: 5AN: 151530Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 73988
ClinVar
Submissions by phenotype
Severe combined immunodeficiency due to LAT deficiency Pathogenic:1
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at