10-101002864-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001318100.2(LZTS2):āc.326A>Gā(p.Asp109Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000496 in 1,613,748 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251214Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135830
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461508Hom.: 1 Cov.: 32 AF XY: 0.0000564 AC XY: 41AN XY: 727062
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.326A>G (p.D109G) alteration is located in exon 2 (coding exon 1) of the LZTS2 gene. This alteration results from a A to G substitution at nucleotide position 326, causing the aspartic acid (D) at amino acid position 109 to be replaced by a glycine (G). 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