10-101003745-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001318100.2(LZTS2):c.647C>T(p.Thr216Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,612,860 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
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LZTS2 | ENST00000454422.2 | c.647C>T | p.Thr216Met | missense_variant | Exon 3 of 5 | 2 | NM_001318100.2 | ENSP00000416972.2 | ||
LZTS2 | ENST00000370220.1 | c.647C>T | p.Thr216Met | missense_variant | Exon 2 of 4 | 1 | ENSP00000359240.1 | |||
LZTS2 | ENST00000370223.7 | c.647C>T | p.Thr216Met | missense_variant | Exon 3 of 5 | 1 | ENSP00000359243.3 | |||
LZTS2 | ENST00000426584.5 | c.647C>T | p.Thr216Met | missense_variant | Exon 3 of 3 | 3 | ENSP00000407713.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 247818Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134532
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1460642Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726654
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.647C>T (p.T216M) alteration is located in exon 3 (coding exon 2) of the LZTS2 gene. This alteration results from a C to T substitution at nucleotide position 647, causing the threonine (T) at amino acid position 216 to be replaced by a methionine (M). 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