chr9-132911540-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_Very_StrongBP7BS2_Supporting
The NM_000368.5(TSC1):c.942G>A(p.Thr314Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00001 in 1,596,320 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 (★★).
Frequency
Consequence
NM_000368.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSC1 | ENST00000298552.9 | c.942G>A | p.Thr314Thr | synonymous_variant | Exon 10 of 23 | 1 | NM_000368.5 | ENSP00000298552.3 | ||
TSC1 | ENST00000490179.4 | c.942G>A | p.Thr314Thr | synonymous_variant | Exon 11 of 24 | 3 | ENSP00000495533.2 |
Frequencies
GnomAD3 genomes AF: 0.0000356 AC: 5AN: 140584Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251250Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135776
GnomAD4 exome AF: 0.00000756 AC: 11AN: 1455624Hom.: 0 Cov.: 33 AF XY: 0.00000967 AC XY: 7AN XY: 723992
GnomAD4 genome AF: 0.0000355 AC: 5AN: 140696Hom.: 0 Cov.: 29 AF XY: 0.0000297 AC XY: 2AN XY: 67230
ClinVar
Submissions by phenotype
not specified Benign:1
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Tuberous sclerosis syndrome Benign:1
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not provided Benign:1
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Tuberous sclerosis 1 Benign:1
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Hereditary cancer-predisposing syndrome Benign:1
This alteration is classified as likely 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at