rs5901000
Your query was ambiguous. Multiple possible variants found:
- chr9-132897613-GAAAAAAAAAAAA-G
- chr9-132897613-GAAAAAAAAAAAA-GAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAAA
- chr9-132897613-GAAAAAAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAACTAGAATAATTAATTAAAAAAAAAAAAAAA
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_000368.5(TSC1):c.2626-15_2626-4delTTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 0)
Consequence
TSC1
NM_000368.5 splice_region, intron
NM_000368.5 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.25
Genes affected
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
Variant 9-132897613-GAAAAAAAAAAAA-G is Benign according to our data. Variant chr9-132897613-GAAAAAAAAAAAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 2707227.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSC1 | ENST00000298552.9 | c.2626-15_2626-4delTTTTTTTTTTTT | splice_region_variant, intron_variant | Intron 20 of 22 | 1 | NM_000368.5 | ENSP00000298552.3 | |||
TSC1 | ENST00000490179.4 | c.2626-15_2626-4delTTTTTTTTTTTT | splice_region_variant, intron_variant | Intron 21 of 23 | 3 | ENSP00000495533.2 |
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD3 genomes
Cov.:
0
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 0
GnomAD4 genome
Cov.:
0
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Tuberous sclerosis 1 Benign:1
Jan 05, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.