Our verdict is Benign. The variant received -11 ACMG points: 2P and 13B. PM1BP4BP6_Very_StrongBS2
The NM_000368.5(TSC1):c.593A>G(p.Asn198Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,150 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. N198N) has been classified as Likely benign.
TSC1 (HGNC:12362): (TSC complex subunit 1) This gene is a tumor suppressor gene that encodes the growth inhibitory protein hamartin. The encoded protein interacts with and stabilizes the GTPase activating protein tuberin. This hamartin-tuberin complex negatively regulates mammalian target of rapamycin complex 1 (mTORC1) signaling which is a major regulator of anabolic cell growth. This protein also functions as a co-chaperone for Hsp90 that inhibits its ATPase activity. This protein functions as a facilitator of Hsp90-mediated folding of kinase and non-kinase clients, including TSC2 and thereby preventing their ubiquitination and proteasomal degradation. Mutations in this gene have been associated with tuberous sclerosis and lymphangioleiomyomatosis. [provided by RefSeq, May 2022]
TSC1 Gene-Disease associations (from GenCC):
tuberous sclerosis
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
tuberous sclerosis 1
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, PanelApp Australia, Genomics England PanelApp, G2P, Labcorp Genetics (formerly Invitae)
lung lymphangioleiomyomatosis
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
tuberous sclerosis complex
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Our verdict: Benign. The variant received -11 ACMG points.
PM1
In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 4 benign, 25 uncertain in NM_000368.5
BP4
Computational evidence support a benign effect (MetaRNN=0.32038626).
BP6
Variant 9-132921889-T-C is Benign according to our data. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-132921889-T-C is described in CliVar as Benign/Likely_benign. Clinvar id is 237723.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
This variant is considered likely benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance. -
Jan 22, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Hereditary cancer-predisposing syndromeBenign:2
Dec 07, 2021
Ambry Genetics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Gain of helix (P = 0.0425);.;Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);.;.;Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);.;Gain of helix (P = 0.0425);.;Gain of helix (P = 0.0425);