chr10-101002682-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001318100.2(LZTS2):c.144C>T(p.His48=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000216 in 1,609,760 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 Benign (★).
Frequency
Genomes: 𝑓 0.0013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
LZTS2
NM_001318100.2 synonymous
NM_001318100.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.95
Genes affected
LZTS2 (HGNC:29381): (leucine zipper tumor suppressor 2) The protein encoded by this gene belongs to the leucine zipper tumor suppressor family of proteins, which function in transcription regulation and cell cycle control. This family member can repress beta-catenin-mediated transcriptional activation and is a negative regulator of the Wnt signaling pathway. It negatively regulates microtubule severing at centrosomes, and is necessary for central spindle formation and cytokinesis completion. It is implicated in cancer, where it may inhibit cell proliferation and decrease susceptibility to tumor development. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 10-101002682-C-T is Benign according to our data. Variant chr10-101002682-C-T is described in ClinVar as [Benign]. Clinvar id is 736827.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.95 with no splicing effect.
BS2
High AC in GnomAd4 at 193 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LZTS2 | NM_001318100.2 | c.144C>T | p.His48= | synonymous_variant | 2/5 | ENST00000454422.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LZTS2 | ENST00000454422.2 | c.144C>T | p.His48= | synonymous_variant | 2/5 | 2 | NM_001318100.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00123 AC: 187AN: 152240Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000296 AC: 73AN: 246720Hom.: 0 AF XY: 0.000217 AC XY: 29AN XY: 133690
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GnomAD4 exome AF: 0.000106 AC: 155AN: 1457402Hom.: 0 Cov.: 32 AF XY: 0.0000938 AC XY: 68AN XY: 724682
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GnomAD4 genome AF: 0.00127 AC: 193AN: 152358Hom.: 0 Cov.: 33 AF XY: 0.00119 AC XY: 89AN XY: 74506
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 30, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at