Variant classification summary

NM_000546.5:c.684C>G

TP53 · NP_000537.3:p.(Asp228Glu) · NM_000546.5

GRCh37: chr17:7577597 G>C · GRCh38: chr17:7674279 G>C

Gene: TP53 Transcript: NM_000546.5

Final call

Likely Benign

PM2 supporting BS3 strong benign BP4 moderate

Variant details

Gene

TP53

Transcript

NM_000546.5

Protein

NP_000537.3:p.(Asp228Glu)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000546.5:c.684C>G (p.Asp228Glu) is a missense variant in exon 7 of TP53.

2

The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_Supporting; +1 point).

3

Functional evidence from the TP53 VCEP Functional-worksheet demonstrates the variant retains wild-type-like function: Kato et al. assay shows Functional activity, and all eligible assays (Giacomelli, Kotler, Kawaguchi) report no loss of function (BS3; -4 points).

4

In silico evidence supports a benign interpretation: BayesDel score is -0.133538 (Class C0), and SpliceAI predicts no splicing impact (max delta 0.00). The VCEP PP3-BP4-codes spreadsheet assigns BP4_moderate (-2 points).

5

Codon 228 is not among the VCEP-defined hotspot codons (175, 245, 248, 249, 273, 282), and the variant is not listed in cancerhotspots.org; PM1 is not met.

6

PP3 is not met per VCEP in silico flowchart: BayesDel score does not meet the ≥0.16 threshold and aGVGD class is C0.

7

PS3 is not met: the functional evidence favors a benign interpretation; the VCEP pre-assigned code is BS3, not PS3.

8

Total points: PM2_Supporting (+1) + BS3 (-4) + BP4_Moderate (-2) = -5. Per the Tavtigian Bayesian point-based framework (TP53 VCEP v2.4.0), a score of -5 falls in the Likely Benign range (-6 to -2).

9

This variant has been reported in ClinVar as Uncertain significance by 5 clinical laboratories and as Likely benign by 1 clinical laboratory (ClinVar ID: 926556).

10

COSMIC reports 6 somatic occurrences (COSV52662428). OncoKB classifies the variant as Likely Oncogenic with likely loss-of-function effect, which is inconsistent with the VCEP functional data showing retained function; the VCEP functional worksheet takes precedence for germline classification.

11

No de novo, segregation, proband, or case-control data are available; PS2, PS4, PP1, PP4, BS2, and BS4 remain unassessed.

Final determination: Per the TP53 VCEP v2.4.0 Tavtigian Bayesian point-based framework, a total score of -5 (PM2_Supporting +1, BS3 -4, BP4_Moderate -2) falls within the Likely Benign range (-6 to -2) under Rule4.

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 restricted to null variants (nonsense, frameshift, canonical ±1,2 splice sites, initiation codon, exon deletions) per the TP53 VCEP PVS1 flowchart. NM_000546.5:c.684C>G is a missense variant (p.Asp228Glu) and does not fall into any null-variant category.	pvs1_generic_framework vcep_pvs1_flowchart
PS1	Not assessed	PS1 requires a different nucleotide change resulting in the same amino acid substitution (p.Asp228Glu) that has been classified as Pathogenic or Likely Pathogenic per TP53 VCEP specifications. Nucleotide variant c.684C>A also encodes p.Asp228Glu and is listed in the VCEP PP3-BP4-codes spreadsheet, but its VCEP clinical classification is not available in the case record. Without a VCEP P/LP comparator, PS1 cannot be assessed.	vcep_pp3_bp4_codes
PS2	Not assessed	PS2 requires tallying de novo proband points using the TP53 VCEP LFS cancer scoring table. No de novo observations or proband phenotype data are available for this variant in the case record.
PS3	Not met	PS3 requires evidence of a damaging functional effect. The TP53 VCEP Functional-worksheet assigns BS3 (strong benign functional evidence) for p.Asp228Glu: Kato et al. (PMID:12826609) data show the variant is Functional, and Giacomelli, Kotler, and Kawaguchi assays all report no loss of function (noLOF). The pre-assigned VCEP code is BS3, not PS3 — the variant retains wild-type-like function across all eligible assays.	vcep_functional_worksheet PMID:12826609 PMID:29979965 PMID:30224644
PS4	Not assessed	PS4 requires tallying proband points based on LFS-associated cancer diagnoses per the TP53 VCEP PS4-Points-Table. No proband or cohort data are available for this variant.
PS5	N/A	PS5 is not a criterion in the standard ACMG/AMP 2015 framework and is not defined by the TP53 VCEP specifications version 2.4.0.
PM1	Not met	PM1 requires the variant to be located in a VCEP-defined hotspot codon (175, 245, 248, 249, 273, 282) or listed in cancerhotspots.org with ≥2 somatic occurrences. p.Asp228Glu is at codon 228, which is not among the designated hotspot codons. The variant is not listed in cancerhotspots.org; the hotspot screen reports residue_significant=false and exact_variant_listed=no. Six somatic occurrences are recorded in COSMIC (COSV52662428), but this does not meet the cancerhotspots.org pathway criterion.
PM2	Met	The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, meeting the TP53 VCEP PM2_Supporting threshold of allele frequency <0.00003 (0.003%).	gnomad_v2 gnomad_v4 gnomad_canada
PM3	N/A	PM3 is not applicable per TP53 VCEP specifications (criteria.json: applicability = 'Not applicable'). PM3 applies to recessive disorders; TP53/Li-Fraumeni syndrome is a dominant disorder.	cspec
PM4	N/A	PM4 is not applicable per TP53 VCEP specifications (criteria.json: applicability = 'Not applicable'). PM4 applies to in-frame deletions/insertions and stop-loss variants; this is a missense substitution.	cspec
PM5	Not assessed	PM5 requires a different pathogenic or likely pathogenic missense variant at the same amino acid residue (Asp228) classified per TP53 VCEP specifications. Multiple other missense variants exist at codon 228 (e.g., D228Y, D228H, D228N, D228V, D228G, D228A), and they appear in the VCEP PP3-BP4-codes spreadsheet, but their VCEP clinical classifications (P/LP vs. VUS) are not available in the case record. Without a confirmed VCEP P/LP comparator at this residue, PM5 cannot be assessed.	vcep_pp3_bp4_codes
PM6	N/A	PM6 is not applicable per TP53 VCEP specifications. The VCEP combines de novo assessment under PS2 using a points-based system; PM6 is listed as 'Not applicable' with instruction 'See above for PS2_PM6 combined rule.'	cspec
PP1	Not assessed	PP1 requires cosegregation data (≥3 meioses for supporting, 5-6 for moderate, ≥7 for strong). No cosegregation or family data are available for this variant.
PP2	N/A	PP2 is not applicable per TP53 VCEP specifications (criteria.json: applicability = 'Not applicable').	cspec
PP3	Not met	PP3 for missense variants requires aGVGD Class C65 with BayesDel ≥0.16 (moderate) or Class C25-C55 with BayesDel ≥0.16 (supporting). The VCEP PP3-BP4-codes spreadsheet assigns BP4_moderate to c.684C>G (p.Asp228Glu). The BayesDel score is -0.133538 (Class C0) and SpliceAI max delta is 0.00, both falling well below PP3 thresholds. PP3 is not met; the in silico evidence supports a benign interpretation (see BP4).	vcep_pp3_bp4_codes bayesdel spliceai
PP4	Not assessed	PP4 requires observation of the variant at low variant allele fraction (VAF 5-35%) suggesting somatic mosaicism or constitutional mosaicism. No VAF data are available for this variant in the case record.
PP5	N/A	PP5 is not applicable per TP53 VCEP specifications. The VCEP states: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'	cspec
BA1	Not met	BA1 requires a filtering allele frequency ≥0.001 (0.1%) in any gnomAD continental subpopulation. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. BA1 is not met.	gnomad_v2 gnomad_v4
BS1	Not met	BS1 requires a filtering allele frequency ≥0.0003 (0.03%) but <0.001 in a gnomAD continental subpopulation. The variant is absent from all gnomAD datasets. BS1 is not met.	gnomad_v2 gnomad_v4
BS2	Not assessed	BS2 requires observations in unrelated cancer-free females who have reached at least 60 years of age. No such clinical observations are available for this variant.
BS3	Met	The TP53 VCEP Functional-worksheet pre-assigns BS3 (strong benign functional evidence) for p.Asp228Glu. The variant is Functional in the Kato et al. (PMID:12826609) systematic assay and shows no loss of function (noLOF) across all eligible assays: Giacomelli et al. (PMID:30224644), Kotler et al. (PMID:29979965), and Kawaguchi et al. This meets the VCEP BS3 rule: 'Functional on Kato et al. data AND no loss of function (LOF) by the majority of available eligible assays.'	vcep_functional_worksheet PMID:12826609 PMID:29979965 PMID:30224644
BS4	Not assessed	BS4 requires lack of segregation in affected family members with LFS-associated cancers. No segregation data are available for this variant.
BP1	N/A	BP1 is not applicable per TP53 VCEP specifications. The VCEP states: 'This rule code does not apply to these genes, as truncating variants account for only a portion of disease causing variants.'	cspec
BP2	N/A	BP2 is not applicable per TP53 VCEP specifications (criteria.json: applicability = 'Not applicable'). TP53 is a dominant disorder gene; BP2 (observed in trans with a pathogenic variant) does not apply.	cspec
BP3	N/A	BP3 is not applicable per TP53 VCEP specifications (criteria.json: applicability = 'Not applicable'). BP3 applies to in-frame deletions/insertions in repetitive regions, which does not describe this substitution variant.	cspec
BP4	Met	The variant has a BayesDel score of -0.133538, which is ≤ -0.008, and SpliceAI predicts no splicing impact (max delta = 0.00, which is <0.2). The aGVGD class is C0 (not C65). Per the TP53 VCEP PP3-BP4 missense flowchart: BayesDel ≤ -0.008 + no predicted splicing differences + not C65 = BP4_Moderate. The VCEP PP3-BP4-codes spreadsheet confirms this with a pre-assigned code of BP4_moderate.	vcep_pp3_bp4_codes bayesdel spliceai
BP5	N/A	BP5 is not applicable per TP53 VCEP specifications (criteria.json: applicability = 'Not applicable').	cspec
BP6	N/A	BP6 is not applicable per TP53 VCEP specifications. The VCEP states: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'	cspec
BP7	N/A	BP7 applies to synonymous (silent) or intronic variants with no predicted splicing impact. NM_000546.5:c.684C>G is a missense variant (p.Asp228Glu), not a synonymous or intronic variant.

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