NM_000368.5:c.1438+6G>A

TSC1 · NP_000359.1:p.? · NM_000368.5

GRCh37: chr9:135782112 C>T · GRCh38: chr9:132906725 C>T

Gene: TSC1 Transcript: NM_000368.5

Final call

VUS

PM2 supporting BP6 supporting benign

Variant details

Gene

TSC1

Transcript

NM_000368.5

Protein

NP_000359.1:p.?

gnomAD AF

0.00015081233855942564 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_000368.5:c.1438+6G>A is present in gnomAD at very low allele frequency (0.010% in v2.1, 0.015% in v4.1; 28–243 alleles, no homozygotes), meeting PM2 at supporting strength.

The variant is reported in ClinVar (ID 48782) with 10 of 15 clinical laboratory submissions classifying as Benign or Likely Benign, meeting BP6 at supporting benign strength. No submission classifies as Pathogenic.

SpliceAI predicts no significant splicing impact (max delta score 0.10). No other computational or functional evidence supports or refutes a deleterious effect.

PS2 (de novo), PS3 (functional), PS4 (case-control), PM6 (assumed de novo), PP1 (cosegregation), PP4 (patient phenotype), BS2 (healthy adults), BS3 (benign functional), BS4 (lack of segregation), BP2 (in trans/cis), and BP5 (alternate molecular basis) could not be assessed due to absence of variant-specific clinical or functional data.

PVS1 is not met: the variant is at the +6 intronic position outside canonical ±1,2 splice sites, and SpliceAI does not predict a splice alteration. The variant does not qualify as a predicted null variant under ClinGen SVI PVS1 recommendations.

Using the generic ACMG/AMP 2015 combination rules (PMID:25741868), the variant has one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP6). The net point score is 0, resulting in a classification of Variant of Uncertain Significance (VUS). This is consistent with the conflicting ClinVar aggregate classification.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Not met	NM_000368.5:c.1438+6G>A is an intronic variant at the donor splice site +6 position, outside the canonical ±1,2 splice consensus. SpliceAI max delta score is 0.10, predicting no significant splice impact. The variant does not qualify as a predicted null variant under the ClinGen SVI PVS1 decision framework (PMC6185798); generic PVS1 framework application is not indicated.	pvs1_generic_framework pvs1_variant_assessment pvs1_gene_context spliceai
PS1	N/A	PS1 requires a same amino acid change as an established pathogenic variant. NM_000368.5:c.1438+6G>A is intronic with no protein-level consequence (p.?), rendering PS1 inapplicable.
PS2	Not assessed	PS2 requires a confirmed de novo occurrence with both parental relationships confirmed in a patient with the disease and no family history. No de novo reports for NM_000368.5:c.1438+6G>A were identified in ClinVar, literature, or de novo databases.
PS3	Not assessed	PS3 requires well-established in vitro or in vivo functional studies demonstrating a damaging effect. No functional studies (RNA analysis, minigene assay, or protein-level evidence) were identified for NM_000368.5:c.1438+6G>A.
PS4	Not assessed	PS4 requires statistically higher prevalence of the variant in affected individuals versus controls. No case-control study or cohort analysis demonstrating enrichment of NM_000368.5:c.1438+6G>A in tuberous sclerosis complex patients was identified.
PS5	N/A	PS5 is not a standard criterion in the ACMG/AMP 2015 generic framework (PMID:25741868). It is used only in select VCEP specifications. No TSC1 VCEP/CSPEC is available for this case. Additionally, the variant is intronic with no amino acid change.
PM1	Not met	PM1 applies to variants located in a mutational hotspot or critical functional domain. NM_000368.5:c.1438+6G>A is intronic and does not map to a defined critical functional domain at the nucleotide or amino acid level. The donor splice region around TSC1 exon 14 is not a recognized mutational hotspot.
PM2	Met	NM_000368.5:c.1438+6G>A is present in gnomAD at very low allele frequency: 0.00999% (28/280,414 alleles, no homozygotes) in v2.1 and 0.01508% (243/1,611,274 alleles, no homozygotes) in v4.1, with grpmax filtering AF of 0.000147 (v2.1) and 0.000179 (v4.1). The allele frequency is well below the 0.1% threshold for PM2 in a dominant disorder gene.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 requires a novel missense change at the same amino acid residue as a known pathogenic missense variant. NM_000368.5:c.1438+6G>A is intronic with no protein-level consequence (p.?). PM5 candidate harvesting was automatically skipped due to unresolvable residue context.	pm5_candidates
PM6	Not assessed	PM6 requires an assumed de novo occurrence without confirmation of paternity and maternity. No de novo reports for NM_000368.5:c.1438+6G>A were identified in any database or publication.
PP1	Not assessed	PP1 requires cosegregation of the variant with disease in multiple affected family members. No segregation data for NM_000368.5:c.1438+6G>A were identified in ClinVar or the literature.
PP2	N/A	PP2 applies to missense variants in genes with a low rate of benign missense variation and a high rate of pathogenic missense variants. NM_000368.5:c.1438+6G>A is intronic and does not produce a missense change.
PP3	Not met	PP3 requires multiple lines of computational evidence supporting a deleterious effect. SpliceAI max delta score is 0.10, which does not predict a significant splicing impact (threshold ≥0.2). REVEL and BayesDel scores are unavailable as the variant is intronic. No in silico tool supports a damaging prediction.	spliceai
PP4	Not assessed	PP4 requires a patient's phenotype or family history to be highly specific for a disease with a single genetic etiology. No individual patient phenotype data are available for NM_000368.5:c.1438+6G>A in the evidence record.
PP5	Not met	PP5 requires a reputable source to report the variant as pathogenic with supporting evidence. The ClinVar aggregate classification for this variant (ID 48782) is conflicting: 10 of 15 submissions classify as Benign or Likely Benign from multiple clinical laboratories, with 1 submission as Uncertain significance. No submission classifies as Pathogenic. The overall ClinVar conclusion does not meet PP5 criteria for a pathogenic assertion.	clinvar
BA1	Not met	BA1 requires an allele frequency >1% in population databases. NM_000368.5:c.1438+6G>A has an allele frequency of 0.010–0.015% in gnomAD, far below the 1% threshold.	gnomad_v2 gnomad_v4
BS1	Not met	BS1 requires an allele frequency >0.3% in population databases for a dominant disorder. NM_000368.5:c.1438+6G>A has an allele frequency of 0.010% (v2.1) and 0.015% (v4.1), below the 0.3% threshold.	gnomad_v2 gnomad_v4
BS2	Not assessed	BS2 requires observation of the variant in a healthy adult individual with full penetrance expected at an early age. No individual-level phenotype data confirming healthy adult carriers of NM_000368.5:c.1438+6G>A are available.
BS3	Not assessed	BS3 requires well-established in vitro or in vivo functional studies showing no damaging effect. No functional studies (splicing assays, RNA analysis, or protein-level experiments) were identified for NM_000368.5:c.1438+6G>A.
BS4	Not assessed	BS4 requires lack of segregation of the variant with disease in affected family members. No family segregation data are available for NM_000368.5:c.1438+6G>A.
BP1	N/A	BP1 applies to missense variants in genes where only truncating variants are known to cause disease. NM_000368.5:c.1438+6G>A is intronic and not a missense variant.
BP2	Not assessed	BP2 requires observation of the variant in trans with a known pathogenic variant in a fully penetrant dominant disorder, or in cis with a pathogenic variant. No such observations have been reported for NM_000368.5:c.1438+6G>A.
BP4	Not met	BP4 requires multiple lines of computational evidence suggesting no impact on gene or gene product. SpliceAI max delta score of 0.10 does not predict a significant splicing alteration, consistent with a benign interpretation. However, ACMG/AMP guidance requires multiple independent lines of computational evidence; SpliceAI is the sole applicable in silico predictor for this intronic variant, and REVEL/BayesDel/HCI are unavailable. A single computational predictor does not meet the multiple-lines requirement for BP4.	spliceai
BP5	Not assessed	BP5 requires identification of an alternate molecular basis for disease in a case where the variant was observed. No data on alternate molecular diagnoses in carriers of NM_000368.5:c.1438+6G>A are available.
BP6	Met	BP6 applies when a reputable source reports the variant as benign with supporting evidence not independently available. ClinVar aggregate classification (ID 48782) for NM_000368.5:c.1438+6G>A is conflicting but predominantly benign: 10 of 15 clinical laboratory submissions classify the variant as Benign (3 submissions), Likely benign (7 submissions), or Likely Benign (1 submission), with only 1 Uncertain significance submission. The weight of clinical laboratory consensus supports application of BP6 at supporting benign strength. No expert panel has reviewed this variant.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants for which splicing prediction algorithms predict no impact and the nucleotide is not highly conserved. NM_000368.5:c.1438+6G>A is intronic, not synonymous. While SpliceAI predicts no splicing impact (delta 0.10), BP7 criteria are explicitly defined for synonymous coding variants and are not directly applicable to intronic variants.

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