Variant classification summary

NM_000546.5:c.370T>g

TP53 · NP_000537.3:p.(Cys124Gly) · NM_000546.5

GRCh37: chr17:7579317 A>C · GRCh38: chr17:7675999 A>C

Gene: TP53 Transcript: NM_000546.5

Final call

VUS

PM2 supporting PP3 moderate

Variant details

Gene

TP53

Transcript

NM_000546.5

Protein

NP_000537.3:p.(Cys124Gly)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000546.5:c.370T>G (p.Cys124Gly) is a missense variant in TP53 exon 4, absent from gnomAD v2.1 and v4.1 (PM2_Supporting met; 1 point).

2

In silico analysis per TP53 VCEP assigns PP3_Moderate: aGVGD Class C65 and BayesDel 0.217 (≥0.16), with no predicted splicing effect (SpliceAI max delta 0.04) (2 points).

3

No functional evidence is applicable per the TP53 VCEP Functional-worksheet, which assigns C124G a code of 'No evidence' due to mixed assay results: Kato partially functional, Giacomelli LOF, Kotler noLOF.

4

The variant has been observed 6 times in somatic cancers (COSMIC COSV52680549) but is not listed in cancerhotspots.org as a statistically significant hotspot, and codon 124 is not among the VCEP-defined PM1 hotspot codons.

5

No proband-level phenotype, cosegregation, de novo, or case-control data are available for this variant. ClinVar reports a single submitter classification of Uncertain significance.

6

Total Tavtigian points: PM2_Supporting (1) + PP3_Moderate (2) = 3 points, falling within the TP53 VCEP VUS range (-1 to 5 points). The variant is classified as Uncertain Significance.

Final determination: Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework yields a total score of 3, which maps to VUS under the specified Tavtigian-style ranges.

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	N/A	PVS1 is not applicable to missense variants; it is reserved for null variants (nonsense, frameshift, canonical splice sites, initiation codon, and CNVs) per the TP53 VCEP PVS1 flowchart. This variant (NM_000546.5:c.370T>G) is a missense substitution producing p.Cys124Gly.
PS1	N/A	PS1 requires a different nucleotide change at the same codon that produces the same amino acid change and has been classified as Pathogenic per TP53 VCEP specifications. The only nucleotide change producing p.Cys124Gly is c.370T>G itself; no alternative nucleotide change yielding C124G with a prior pathogenic classification was identified.
PS2	Not met	No confirmed de novo occurrence of NM_000546.5:c.370T>G with confirmed paternity/maternity has been identified in published literature or databases.
PS3	Not met	The TP53 VCEP Functional-worksheet (Supplementary Table S3) assigns C124G a code of 'No evidence.' The Kato assay showed partially functional activity; Giacomelli showed LOF but Kotler showed noLOF. The mixed results do not meet any PS3 strength threshold: PS3_Strong requires non-functional on Kato + LOF by majority of other assays; PS3_Moderate requires partially functional on Kato + LOF by majority of other assays (only 1 of 2 other assays shows LOF); PS3_Supporting requires non-functional on Kato (C124G is partially functional).	vcep_functional_worksheet
PS4	Not met	No proband data meeting the TP53 VCEP PS4 point system (LFS-associated cancers per proband) is available for this variant. The variant is observed 6 times in COSMIC (somatic) but no germline case-control or prevalence data were identified. The single ClinVar submission classifies the variant as Uncertain significance.	clinvar
PS5	N/A	PS5 is not a criterion defined or used by the TP53 VCEP v2.4.0. The analogous PP5 criterion is explicitly marked as Not Applicable for this VCEP per ClinGen SVI guidance.	cspec
PM1	Not met	Codon 124 is not among the TP53 VCEP-defined mutational hotspot codons (175, 245, 248, 249, 273, 282) for PM1_Moderate. The variant is not listed in cancerhotspots.org as a statistically significant hotspot, so neither PM1_Supporting (2-9 somatic occurrences per cancerhotspots.org) applies.	cspec
PM2	Met	The variant is absent from gnomAD v2.1 and v4.1, meeting the TP53 VCEP PM2_Supporting threshold (allele frequency < 0.003% / 0.00003 in large population databases).	gnomad_v2 gnomad_v4
PM5	Not assessed	Other missense variants exist at codon 124 (e.g., C124R, C124S) but none have been definitively classified as Pathogenic or Likely Pathogenic following TP53 VCEP specifications. The PM5 candidates pipeline returned a false-negative 'not_applicable' recommendation (misclassifying this clearly missense variant as non-missense). Manual review of comparators is needed to determine if any qualify under VCEP PM5 rules (PM5_Strong: ≥2 different pathogenic missense at same residue; PM5_Moderate: 1 pathogenic; PM5_Supporting: 1 likely pathogenic with clinical data).
PM6	N/A	PM6 is marked as Not Applicable by the TP53 VCEP v2.4.0. No de novo data are available for this variant, but the criterion itself is not in use per VCEP specifications.	cspec
PP1	Not met	No published cosegregation data for NM_000546.5:c.370T>G in affected family members has been identified. TP53 VCEP PP1 requires observed cosegregation in ≥3 meioses for Supporting, 5-6 for Moderate, or ≥7 for Strong.
PP2	N/A	PP2 is marked as Not Applicable by the TP53 VCEP v2.4.0.	cspec
PP3	Met	The TP53 VCEP PP3-BP4-codes spreadsheet (Supplementary Table S2) assigns c.370T>G a pre-computed code of PP3_moderate based on aGVGD Class C65 and BayesDel score 0.216879 (≥0.16). SpliceAI max delta score is 0.04, indicating no predicted splicing effect, so in silico evidence is not confounded by splicing.	vcep_pp3_bp4_codes bayesdel spliceai
PP4	Not met	No proband-specific phenotype data or variant allele fraction (VAF) observations meeting the TP53 VCEP PP4 thresholds are available. PP4 requires variant observation with VAF 5-35% (Supporting) or ≥2 independent observations with VAF 5-25% (Moderate).
PP5	N/A	PP5 is explicitly marked as Not Applicable for this VCEP by the ClinGen Sequence Variant Interpretation VCEP Review Committee (TP53 VCEP v2.4.0).	cspec
BA1	Not met	The variant is absent from gnomAD v2.1 and v4.1, so the TP53 VCEP BA1 threshold (filtering allele frequency ≥0.001 / 0.1% in a single continental genetic ancestry group) is not met.	gnomad_v2 gnomad_v4
BS1	Not met	The variant is absent from gnomAD v2.1 and v4.1, so the TP53 VCEP BS1 threshold (filtering allele frequency ≥0.0003 but <0.001 in a single continental genetic ancestry group) is not met.	gnomad_v2 gnomad_v4
BS2	Not met	No data are available regarding unrelated females ≥60 years of age without cancer carrying this variant. BS2 requires ≥2 such individuals for Supporting, 4-7 for Moderate, or ≥8 for Strong, all from a single source.
BS3	Not met	The TP53 VCEP Functional-worksheet assigns C124G a code of 'No evidence.' The Kato assay showed partially functional (not 'Functional') activity, so neither BS3_Strong (requires Functional on Kato + no LOF by majority) nor BS3_Supporting (requires Partially functional on Kato + no LOF by all assays; Giacomelli shows LOF) is met.	vcep_functional_worksheet
BS4	Not met	No reports of non-segregation (apparently healthy individuals carrying the variant in affected families) for c.370T>G have been identified. BS4 requires lack of segregation in affected family members with LFS-associated cancers.
BP1	N/A	BP1 is marked as Not Applicable by the TP53 VCEP v2.4.0.	cspec
BP2	N/A	BP2 is marked as Not Applicable by the TP53 VCEP v2.4.0.	cspec
BP4	Not met	The TP53 VCEP PP3-BP4-codes spreadsheet assigns c.370T>G a code of PP3_moderate, not BP4. The variant has aGVGD Class C65 (most pathogenic class) and BayesDel 0.216879 (≥0.16), which are incompatible with BP4 application. BP4_Moderate requires BayesDel ≤ -0.008; BP4_Supporting requires BayesDel <0.16 and > -0.008.	vcep_pp3_bp4_codes bayesdel
BP5	N/A	BP5 is marked as Not Applicable by the TP53 VCEP v2.4.0.	cspec
BP6	N/A	BP6 is marked as Not Applicable by the TP53 VCEP v2.4.0.	cspec
BP7	N/A	BP7 applies only to synonymous (silent) or intronic variants per the TP53 VCEP PP3/BP4/BP7 flowchart. NM_000546.5:c.370T>G is a missense variant producing p.Cys124Gly and is not eligible for BP7.
BP3	N/A	Variant is a substitution, not an in-frame deletion/insertion in a repetitive region.
PM3	N/A	TP53 is associated with autosomal dominant disease; PM3 (detected in trans with a pathogenic variant) is not applicable.
PM4	N/A	Variant is a missense substitution, not a protein-length changing variant (in-frame deletion/insertion or stop-loss).

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