10-101003864-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001318100.2(LZTS2):c.766G>A(p.Ala256Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,612,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001318100.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LZTS2 | NM_001318100.2 | c.766G>A | p.Ala256Thr | missense_variant | 3/5 | ENST00000454422.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LZTS2 | ENST00000454422.2 | c.766G>A | p.Ala256Thr | missense_variant | 3/5 | 2 | NM_001318100.2 | P1 | |
LZTS2 | ENST00000370220.1 | c.766G>A | p.Ala256Thr | missense_variant | 2/4 | 1 | P1 | ||
LZTS2 | ENST00000370223.7 | c.766G>A | p.Ala256Thr | missense_variant | 3/5 | 1 | P1 | ||
LZTS2 | ENST00000426584.5 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000324 AC: 8AN: 247054Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134494
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460756Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 6AN XY: 726688
GnomAD4 genome AF: 0.000197 AC: 30AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.766G>A (p.A256T) alteration is located in exon 3 (coding exon 2) of the LZTS2 gene. This alteration results from a G to A substitution at nucleotide position 766, causing the alanine (A) at amino acid position 256 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at