NM_000548.5:c.4006-8C>T is an intronic variant at position -8 of exon 34 in TSC2, not predicted to alter splicing (SpliceAI delta = 0.00).1 This variant is present in gnomAD at appreciable population frequencies: v2.1 AF=0.2436% (538/220866 alleles, 5 homozygotes) and v4.1 AF=0.3818% (6017/1575890 alleles, 15 homozygotes), with the highest subpopulation frequency in the European (non-Finnish) group at 0.3946% (v2.1) and 0.4712% (v4.1). These frequencies far exceed the expected prevalence of tuberous sclerosis complex (estimated incidence ~1:6000 to 1:10000 live births), meeting BS1 (strong benign).2 Five homozygotes are observed in gnomAD v2.1 and 15 homozygotes in gnomAD v4.1. TSC is an autosomal dominant disorder with near-complete penetrance and significant morbidity; the presence of homozygotes in a general population database is incompatible with pathogenicity, meeting BS2 (strong benign).3 This variant has been classified as Benign by 14 clinical diagnostic laboratories and as Likely benign by 5 clinical laboratories in ClinVar (Variation ID 49281), meeting BP6 (supporting benign).4 SpliceAI predicts no splicing impact (max delta = 0.00), and the variant is an intronic substitution at a non-canonical splice position, meeting BP4 and BP7 (each supporting benign).5 No variant-specific functional studies, de novo observations, cosegregation data, or case-control studies were identified for this variant. The ClinVar criterion-lead submission (SCV000066333, Tuberous sclerosis database) cited PMID:17304050, but the full text of that publication does not mention NM_000548.5:c.4006-8C>T. Classification: Likely Benign. Benign evidence includes BS1 (strong), BS2 (strong), BP4 (supporting), BP6 (supporting), and BP7 (supporting). No pathogenic or likely pathogenic criteria are met. Under the ACMG/AMP 2015 combining criteria, ≥2 strong benign criteria → Likely Benign.6
TSC2
Final classification
Benign
TSC2 c.4006-8C>T · p.?
TSC2
NM_000548.5:c.4006-8C>T is an intronic variant at position -8 of exon 34 in TSC2, not predicted to alter splicing (SpliceAI delta = 0.00).
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BS1 strong, BS2 strong, BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; combination = 2 strong benign + 3 supporting benign, which maps to Benign.
Classification rationale
BS1BS2BP4BP6BP7
Benign
TSC2 c.4006-8C>T
BS1 + BS2 + BP4 + BP6 + BP7
→
Benign
6
generic_acmg_combination_rules
Gene diagram
· NM_000548.5 · variants mapped to exon structure
TSC2
NM_000548.5
Fetching transcript structure from UCSC…
Applied criteria · 5 met · select any tile
Met
Not met
Not assessed
N/A
Strength
very strong
supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
—
—
—
Rationale
Select a criterion.
Sources
Evidence used
Gaps remaining
Rule
—
Research & evidence
Population frequency · supports benign
gnomAD v4.1
gnomAD v2.1
Population frequency
15
homozygotes observed in gnomAD v4.1. Healthy biallelic carriers are difficult to reconcile with a fully penetrant loss-of-function disease allele.
Overall AF
6017 / 1,575,890
0.38%
Highest · European (non-Finnish)
0.47%
Homozygotes
15
grpmax FAF
0.46%
Allele frequency by ancestry — gnomAD v4.1
observed in 8 of 9 groups
| Ancestry | Allele count | Frequency | Homozygotes |
|---|---|---|---|
| European (non-Finnish) | 5465 / 1,159,748 | 0.47% | 13 |
| Admixed American | 201 / 55,630 | 0.36% | 0 |
| African/African American | 62 / 73,896 | 0.084% | 0 |
| South Asian | 50 / 86,804 | 0.058% | 1 |
| Middle Eastern | 2 / 6,028 | 0.033% | 0 |
| European (Finnish) | 12 / 60,312 | 0.02% | 0 |
| Ashkenazi Jewish | 4 / 28,974 | 0.014% | 0 |
| East Asian | 1 / 42,596 | 0.0023% | 0 |
| Amish | 0 / 912 | — | — |
“
This variant is present in gnomAD v4.1 (AF= 0.00381816; MAF= 0.38182%, 6017/1575890 alleles, homozygotes = 15) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00471223; MAF= 0.47122%, 5465/1159748 alleles, homozygotes = 13); grpmax FAF= 0.0046076.
5
homozygotes observed in gnomAD v2.1. Healthy biallelic carriers are difficult to reconcile with a fully penetrant loss-of-function disease allele.
Overall AF
538 / 220,866
0.24%
Highest · European (non-Finnish)
0.39%
Homozygotes
5
grpmax FAF
0.38%
Allele frequency by ancestry — gnomAD v2.1
observed in 7 of 8 groups
| Ancestry | Allele count | Frequency | Homozygotes |
|---|---|---|---|
| European (non-Finnish) | 365 / 92,500 | 0.39% | 4 |
| Admixed American | 116 / 30,504 | 0.38% | 1 |
| Remaining individuals | 21 / 6,130 | 0.34% | 0 |
| African/African American | 17 / 19,760 | 0.086% | 0 |
| South Asian | 14 / 25,778 | 0.054% | 0 |
| European (Finnish) | 4 / 20,992 | 0.019% | 0 |
| East Asian | 1 / 15,960 | 0.0063% | 0 |
| Ashkenazi Jewish | 0 / 9,242 | — | — |
“
This variant is present in gnomAD v2.1 (AF= 0.00243587; MAF= 0.24359%, 538/220866 alleles, homozygotes = 5) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00394595; MAF= 0.39459%, 365/92500 alleles, homozygotes = 4); grpmax FAF= 0.00380144.
“
This variant is absent from gnomAD-Canada.
ClinVar
This variant has been reported in ClinVar as Benign (14 clinical laboratories) and as Likely benign (5 clinical laboratories). (ClinVarID = 49281)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional
No data
No calibrated functional assay or RNA evidence was identified for this variant.
COSMIC
Somatic evidence
COSMIC
This variant has previously been reported in somatic cancers (COSMIC; COSV104573703, n = 2 times).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
Literature · 13 PMIDs triaged · 8 high-priority
13papers screened
Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
15798777 ↗
de novo
Mutational analysis of the TSC1 and TSC2 genes in a diagnostic setting: genotype--phenotype correlations and comparison of diagnostic DNA techniques in Tuberous Sclerosis Complex.
Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterised by the development of hamartomas in multiple organs and tissues. TSC is caused by mutations in either the TSC1 or TSC2 gene. We searched for mutations in both genes in a cohort of 490 patients diagnosed with or suspected of having TSC using a combination of denaturing gradient gel electrophoresis, single-strand confor
PM6PP5PS2PS4
17304050 ↗
de novo
Genotype/phenotype correlation in 325 individuals referred for a diagnosis of tuberous sclerosis complex in the United States.
Tuberous sclerosis complex is an autosomal dominant neurocutaneous disorder marked by hamartoma growth in multiple organ systems. We performed mutational analyses on 325 individuals with definite tuberous sclerosis complex diagnostic status. We identified mutations in 72% (199/257) of de novo and 77% (53/68) of familial cases, with 17% of mutations in the TSC1 gene and 50% in the TSC2 gene. There
PM6PP5PS2PS4
25741868 ↗
functional
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic
BS3PP5PS3PS4
26467025 ↗
functional
A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.
We developed a rules-based scoring system to classify DNA variants into five categories including pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, and benign. Over 16,500 pathogenicity assessments on 11,894 variants from 338 genes were analyzed for pathogenicity based on prediction tools, population frequency, co-occurrence, segregation, and functional studies
BS3PP5PS3PS4
23519317 ↗
case observation
Clinical genetics evaluation in identifying the etiology of autism spectrum disorders: 2013 guideline revisions.
The autism spectrum disorders are a collective of conditions that have in common impaired socialization and communication in association with stereotypic behaviors. The reported incidence of autism spectrum disorders has increased dramatically over the past two decades. In addition, increased attention has been paid to these conditions by both lay and professional groups. These trends have resulte
PP5PS4
23788249 ↗
case observation
ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
In clinical exome and genome sequencing, there is a potential for the recognition and reporting of incidental or secondary findings unrelated to the indication for ordering the sequencing but of medical value for patient care. The American College of Medical Genetics and Genomics (ACMG) recently published a policy statement on clinical sequencing that emphasized the importance of alerting the pati
PP5PS4
25356965 ↗
case observation
ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing.
These recommendations are designed primarily as an educational resource for medical geneticists and other health-care providers to help them provide quality medical genetics services. Adherence to these recommendations does not necessarily ensure a successful medical outcome. These recommendations should not be considered inclusive of all proper procedures and tests or exclusive of other procedure
PP5PS4
28492532 ↗
background review
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
PP5PS4
Sources & reference links