16-28985699-CCT-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001014987.2(LAT):c.101-9_101-8delCT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,508 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001014987.2 splice_region, intron
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAT | NM_001014987.2 | c.101-9_101-8delCT | splice_region_variant, intron_variant | Intron 1 of 11 | ENST00000395456.7 | NP_001014987.1 | ||
LAT | NM_001014989.2 | c.209-9_209-8delCT | splice_region_variant, intron_variant | Intron 2 of 12 | NP_001014989.2 | |||
LAT | NM_014387.4 | c.101-9_101-8delCT | splice_region_variant, intron_variant | Intron 1 of 10 | NP_055202.1 | |||
LAT | NM_001014988.2 | c.101-9_101-8delCT | splice_region_variant, intron_variant | Intron 1 of 11 | NP_001014988.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461508Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 727066
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change falls in intron 1 of the LAT gene. It does not directly change the encoded amino acid sequence of the LAT protein. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with LAT-related conditions. This variant is not present in population databases (gnomAD no frequency). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.