rs118203516
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_000368.5(TSC1):c.1333+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000346 in 1,611,646 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000368.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSC1 | ENST00000298552.9 | c.1333+13C>T | intron_variant | Intron 13 of 22 | 1 | NM_000368.5 | ENSP00000298552.3 | |||
TSC1 | ENST00000490179.4 | c.1333+13C>T | intron_variant | Intron 14 of 23 | 3 | ENSP00000495533.2 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000438 AC: 110AN: 251262Hom.: 0 AF XY: 0.000582 AC XY: 79AN XY: 135820
GnomAD4 exome AF: 0.000362 AC: 528AN: 1459374Hom.: 4 Cov.: 30 AF XY: 0.000410 AC XY: 298AN XY: 726186
GnomAD4 genome AF: 0.000190 AC: 29AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74458
ClinVar
Submissions by phenotype
Tuberous sclerosis 1 Benign:2
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Hereditary cancer-predisposing syndrome Uncertain:1
The c.1333+13C>T intronic alteration consists of a C to T substitution 3 nucleotides after coding exon 11 in the TSC1 gene. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Lymphangiomyomatosis;C1846385:Isolated focal cortical dysplasia type II;C1854465:Tuberous sclerosis 1 Benign:1
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Tuberous sclerosis syndrome Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at