10-101003771-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001318100.2(LZTS2):āc.673C>Gā(p.Leu225Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000924 in 1,613,142 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LZTS2 | ENST00000454422.2 | c.673C>G | p.Leu225Val | missense_variant | Exon 3 of 5 | 2 | NM_001318100.2 | ENSP00000416972.2 | ||
LZTS2 | ENST00000370220.1 | c.673C>G | p.Leu225Val | missense_variant | Exon 2 of 4 | 1 | ENSP00000359240.1 | |||
LZTS2 | ENST00000370223.7 | c.673C>G | p.Leu225Val | missense_variant | Exon 3 of 5 | 1 | ENSP00000359243.3 | |||
LZTS2 | ENST00000426584.5 | c.673C>G | p.Leu225Val | missense_variant | Exon 3 of 3 | 3 | ENSP00000407713.1 |
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152236Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000214 AC: 53AN: 248038Hom.: 0 AF XY: 0.000156 AC XY: 21AN XY: 134598
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1460788Hom.: 0 Cov.: 31 AF XY: 0.0000688 AC XY: 50AN XY: 726702
GnomAD4 genome AF: 0.000308 AC: 47AN: 152354Hom.: 1 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.673C>G (p.L225V) alteration is located in exon 3 (coding exon 2) of the LZTS2 gene. This alteration results from a C to G substitution at nucleotide position 673, causing the leucine (L) at amino acid position 225 to be replaced by a valine (V). 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