10-101002671-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001318100.2(LZTS2):āc.133C>Gā(p.Pro45Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000416 in 1,609,048 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 (ā ).
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.133C>G | p.Pro45Ala | missense_variant | 2/5 | ENST00000454422.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LZTS2 | ENST00000454422.2 | c.133C>G | p.Pro45Ala | missense_variant | 2/5 | 2 | NM_001318100.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246018Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133356
GnomAD4 exome AF: 0.0000426 AC: 62AN: 1456824Hom.: 0 Cov.: 32 AF XY: 0.0000345 AC XY: 25AN XY: 724366
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2023 | The c.133C>G (p.P45A) alteration is located in exon 2 (coding exon 1) of the LZTS2 gene. This alteration results from a C to G substitution at nucleotide position 133, causing the proline (P) at amino acid position 45 to be replaced by an alanine (A). 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