10-101003609-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001318100.2(LZTS2):c.511G>A(p.Gly171Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000223 in 1,598,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000914 AC: 22AN: 240658Hom.: 0 AF XY: 0.000100 AC XY: 13AN XY: 129410
GnomAD4 exome AF: 0.000239 AC: 345AN: 1446172Hom.: 0 Cov.: 31 AF XY: 0.000240 AC XY: 172AN XY: 717288
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.511G>A (p.G171R) 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 511, causing the glycine (G) at amino acid position 171 to be replaced by an arginine (R). 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