8-20249712-A-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_021020.5(LZTS1):c.*10T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000374 in 1,589,626 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 Benign (no stars).
Frequency
Consequence
NM_021020.5 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LZTS1 | ENST00000381569 | c.*10T>A | 3_prime_UTR_variant | Exon 4 of 4 | 5 | NM_021020.5 | ENSP00000370981.1 | |||
LZTS1 | ENST00000265801 | c.*10T>A | 3_prime_UTR_variant | Exon 3 of 3 | 1 | ENSP00000265801.6 | ||||
LZTS1 | ENST00000522290.5 | c.*10T>A | downstream_gene_variant | 1 | ENSP00000429263.1 |
Frequencies
GnomAD3 genomes AF: 0.00197 AC: 300AN: 152080Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000537 AC: 128AN: 238568Hom.: 1 AF XY: 0.000394 AC XY: 51AN XY: 129406
GnomAD4 exome AF: 0.000206 AC: 296AN: 1437428Hom.: 2 Cov.: 31 AF XY: 0.000182 AC XY: 130AN XY: 712864
GnomAD4 genome AF: 0.00196 AC: 299AN: 152198Hom.: 3 Cov.: 33 AF XY: 0.00198 AC XY: 147AN XY: 74418
ClinVar
Submissions by phenotype
LZTS1-related disorder Benign:1
This variant is classified as 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