16-28985396-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001014989.2(LAT):c.87C>T(p.Ser29Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000295 in 1,612,758 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001014989.2 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAT | NM_001014987.2 | c.-22C>T | 5_prime_UTR_variant | Exon 1 of 12 | ENST00000395456.7 | NP_001014987.1 | ||
LAT | NM_001014989.2 | c.87C>T | p.Ser29Ser | synonymous_variant | Exon 2 of 13 | NP_001014989.2 | ||
LAT | NM_014387.4 | c.-22C>T | 5_prime_UTR_variant | Exon 1 of 11 | NP_055202.1 | |||
LAT | NM_001014988.2 | c.-22C>T | 5_prime_UTR_variant | Exon 1 of 12 | NP_001014988.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000572 AC: 143AN: 250060Hom.: 1 AF XY: 0.000784 AC XY: 106AN XY: 135234
GnomAD4 exome AF: 0.000305 AC: 446AN: 1460490Hom.: 5 Cov.: 33 AF XY: 0.000453 AC XY: 329AN XY: 726578
GnomAD4 genome AF: 0.000197 AC: 30AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74442
ClinVar
Submissions by phenotype
LAT-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at