Variant classification summary

NM_000546.5:c.422G>A

TP53 · NP_000537.3:p.(Cys141Tyr) · NM_000546.5

GRCh37: chr17:7578508 C>T · GRCh38: chr17:7675190 C>T

Gene: TP53 Transcript: NM_000546.5

Final call

Likely Pathogenic

PS3 strong PM2 supporting PP3 moderate

Variant details

Gene

TP53

Transcript

NM_000546.5

Protein

NP_000537.3:p.(Cys141Tyr)

gnomAD AF

1.8585656333867775e-06 (v4.1)

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000546.5:c.422G>A (p.Cys141Tyr) is a missense variant in exon 5 of TP53.

2

This variant is extremely rare in population databases: gnomAD v4.1 total allele frequency = 1.86e-6 (3/1,614,148 alleles), meeting PM2_Supporting (VCEP threshold <0.00003). It is absent from gnomAD v2.1 and gnomAD-Canada.

3

Functional studies demonstrate complete loss of function. The variant is non-functional in the Kato transactivation assay, and all additional eligible assays (Funk, Giacomelli, Kotler) show LOF, satisfying PS3 (strong) per TP53 VCEP specifications.

4

In silico predictions strongly support a deleterious effect: BayesDel score = 0.568676, aGVGD Class C65, REVEL = 0.897. The VCEP PP3-BP4-codes.xlsx assigns PP3_moderate for c.422G>A.

5

SpliceAI predicts no splicing impact (max delta = 0.00), confirming this variant is assessed as a missense change without splicing aberration.

6

The variant has been reported in ClinVar as Pathogenic by 5 clinical laboratories and Likely Pathogenic by 2, and has been observed 182 times in COSMIC somatic cancer database.

7

Combined Tavtigian point score (TP53 VCEP v2.4.0): PS3 (strong) = +4, PP3_moderate = +2, PM2_Supporting = +1. Total = +7 points, which falls in the Likely Pathogenic range (6-9 points).

8

Additional criteria (PS4, PS2, PP1) could not be assessed due to lack of proband-level cancer phenotype data, de novo observations, and cosegregation data in the available evidence. If PS4 evidence becomes available with ≥4 points (≥1 proband with strongly associated LFS cancer), the total would reach ≥10 points, reclassifying the variant as Pathogenic.

Final determination: Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework yields a total score of 7, which maps to Likely Pathogenic 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. This variant (c.422G>A, p.Cys141Tyr) is a missense substitution, not a null variant (nonsense, frameshift, or canonical ±1,2 splice site). The VCEP PVS1 flowchart applies only to null variants. SpliceAI predicts no splicing impact (max delta = 0.00).	spliceai pvs1_variant_assessment
PS1	Not assessed	PS1 requires a different nucleotide change at the same codon that produces the identical amino acid change (e.g., c.421T>A also yields p.Cys141Tyr) and has been previously classified as Pathogenic or Likely Pathogenic per TP53 VCEP specifications. No such comparator variant was identified in the available evidence. Without a qualifying comparator, PS1 cannot be applied.
PS2	Not assessed	No de novo evidence was identified for this variant. The exploratory evidence search for PS2 did not return results within the available timeframe. No papers with confirmed de novo observations of c.422G>A were found in full-text review. The VCEP PS2 scoring system (1 pt = Supporting, 2-3 pts = Moderate, 4-7 pts = Strong, ≥8 pts = Very Strong) requires proband cancer data with LFS-associated phenotypes.
PS3	Met	The TP53 VCEP Functional-worksheet.xlsx (Supplementary Table S3) assigns PS3 to C141Y. Kato assay: Non-functional. Additional eligible assays: Funk — LOF, Giacomelli — LOF, Kotler — LOF. This satisfies the VCEP PS3 rule: 'Non-functional on Kato et al. data AND loss of function (LOF) by the majority of other eligible assays' (3 of 3 non-Kato assays show LOF), conferring PS3 (strong). The variant is non-functional across all tested platforms.	vcep_functional_worksheet PMID:12826609
PS4	Not assessed	PS4 requires proband counts with LFS-associated cancer phenotypes to calculate points per the VCEP PS4-Points-Table (strongly associated cancers = 4 pts, moderately associated = 2 pts per proband). The variant has been reported in ClinVar as Pathogenic by 5 clinical laboratories and Likely Pathogenic by 2, citing papers including PMID:10589545 and PMID:11370630. However, the specific variant was not confirmed in any available full-text publication. Without verified proband-level cancer phenotype data, PS4 points cannot be calculated.	clinvar
PS5	N/A	PS5 (same amino acid change as a previously established pathogenic variant) is not defined in the TP53 VCEP v2.4.0 criteria. The VCEP subsumes same-residue comparator logic under PM5 (different missense at same residue) and PS1 (same amino acid via different nucleotide change). No PS5 rules exist in the VCEP framework.	cspec
PM1	Not met	PM1 is not met. Codon 141 is not one of the six VCEP-defined hotspot codons (175, 245, 248, 249, 273, 282). The alternative cancerhotspots.org pathway requires the same amino acid change (C141Y) to have ≥10 somatic occurrences (Moderate) or 2-9 (Supporting). The exact variant C141Y is not individually listed in cancerhotspots.org (exact_variant_listed: 'no'); the residue-level hotspot signal alone does not satisfy the VCEP PM1 rule which requires the specific amino acid change count.	cspec
PM2	Met	PM2_Supporting is met per VCEP specifications. gnomAD v4.1 total allele frequency = 1.86e-6 (0.000186%), which is well below the VCEP cutoff of <0.00003 (0.003%). In the highest subpopulation (European non-Finnish), AF = 2.54e-6 with 3 alleles across 1,180,016 alleles (<0.00004). The variant is absent from gnomAD v2.1 and gnomAD-Canada. The VCEP requires PM2 to be applied at supporting level for TP53.	gnomad_v4 gnomad_v2 cspec
PM5	Not met	PM5 is not met. The pipeline searched for other missense variants at codon 141 (Cys) classified as Pathogenic or Likely Pathogenic per TP53 VCEP specifications. Zero qualifying comparator variants were identified. PM5_Strong requires ≥2 different pathogenic missense variants at the same residue; PM5_Moderate requires 1 pathogenic; PM5_Supporting requires 1 likely pathogenic with clinical data. None were found.	pm5_candidates
PM6	N/A	PM6 is declared not applicable by the TP53 VCEP v2.4.0. De novo evidence is assessed under the PS2 criterion per VCEP specifications.	cspec
PP1	Not assessed	No cosegregation data is available for this variant. PP1 per VCEP requires observed cosegregation in 3-4 meioses (Supporting), 5-6 meioses (Moderate), or ≥7 meioses (Strong) across one or more families. No family pedigree or segregation studies mentioning c.422G>A were identified in the available evidence. The exploratory search for PP1 did not return results.
PP2	N/A	PP2 is declared not applicable by the TP53 VCEP v2.4.0.	cspec
PP3	Met	The TP53 VCEP PP3-BP4-codes.xlsx (Supplementary Table S2) assigns PP3_moderate to c.422G>A (p.Cys141Tyr). BayesDel score = 0.568676 (≥0.16), aGVGD Class C65, and SpliceAI max delta = 0.00 (no predicted splicing effect, so the missense in silico rules apply directly). This satisfies the VCEP PP3_moderate rule: aGVGD Class C65 and BayesDel score ≥0.16. REVEL score = 0.897, consistent with a damaging prediction.	vcep_pp3_bp4_codes bayesdel revel spliceai
PP4	Not assessed	No variant allele fraction (VAF) data is available to assess PP4. The VCEP PP4 rule requires observation of the variant with VAF 5-35% (Supporting) or ≥2 independent observations with VAF 5-25% (Moderate), as a surrogate for constitutional mosaicism or clonal hematopoiesis assessment. No VAF data for c.422G>A was found in the evidence.
PP5	N/A	PP5 is declared not applicable by the TP53 VCEP v2.4.0. Per the VCEP: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'	cspec
BA1	Not met	BA1 is not met. The VCEP BA1 threshold requires filtering allele frequency (FAF) ≥0.001 (0.1%) in a gnomAD continental subpopulation with ≥2,000 alleles and ≥2 alleles present (excluding founder populations). gnomAD v4.1 grpmax FAF = 6.8e-7, four orders of magnitude below the BA1 threshold. The variant is extremely rare in all populations.	gnomad_v4 cspec
BS1	Not met	BS1 is not met. The VCEP BS1 threshold requires FAF ≥0.0003 (0.03%) but <0.001 in a qualifying gnomAD subpopulation. gnomAD v4.1 grpmax FAF = 6.8e-7, approximately three orders of magnitude below the BS1 lower bound.	gnomad_v4 cspec
BS2	Not assessed	No data are available on healthy females ≥60 years of age without cancer who carry this variant. The VCEP BS2 rule requires ≥8 (Strong), 4-7 (Moderate), or 2-3 (Supporting) unrelated females aged ≥60 without cancer, all from a single source. No such observations were found in the evidence.
BS3	Not met	BS3 is not met. The TP53 VCEP Functional-worksheet.xlsx assigns PS3 (not BS3) for C141Y. The variant is non-functional on Kato and shows LOF across all tested eligible assays (Funk, Giacomelli, Kotler). Per VCEP rules, BS3 requires functional or partially functional status on Kato AND no LOF by the majority of available assays — the opposite of what is observed. Functional evidence supports pathogenicity, not benign effect.	vcep_functional_worksheet PMID:12826609
BS4	Not assessed	No segregation data demonstrating lack of segregation in affected family members is available. The VCEP BS4 rule requires observation of the variant not segregating with LFS-associated cancers in affected family members. The exploratory search for BS4 evidence did not return results.
BP1	N/A	BP1 is declared not applicable by the TP53 VCEP v2.4.0.	cspec
BP2	N/A	BP2 is declared not applicable by the TP53 VCEP v2.4.0.	cspec
BP4	Not met	BP4 is not met. The VCEP PP3-BP4-codes.xlsx assigns PP3_moderate to c.422G>A, which precludes BP4. BayesDel score = 0.568676, far above the BP4_Supporting threshold (<0.16 and >-0.008) and the BP4_Moderate threshold (≤-0.008). SpliceAI max delta = 0.00 (no predicted splicing effect). The variant is strongly predicted damaging by all in silico tools.	vcep_pp3_bp4_codes bayesdel spliceai
BP5	N/A	BP5 is declared not applicable by the TP53 VCEP v2.4.0.	cspec
BP6	N/A	BP6 is declared not applicable by the TP53 VCEP v2.4.0.	cspec
BP7	N/A	BP7 is not applicable to missense variants. BP7 per VCEP applies only to synonymous (silent) variants outside the core splice motif or intronic variants at or beyond +7 to -21 positions for which SpliceAI predicts no splicing impact (≤0.1). This is a missense variant producing p.Cys141Tyr.	cspec spliceai
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions without known function. c.422G>A is a missense substitution, not an in-frame indel.
PM3	N/A	PM3 applies to recessive disorders where a variant is detected in trans with a pathogenic variant. TP53-associated Li-Fraumeni syndrome is an autosomal dominant condition; PM3 is not applicable.
PM4	N/A	PM4 applies to in-frame deletions/insertions or stop-loss variants. c.422G>A is a missense substitution, not a protein-length-altering variant. VCEP also declares PM4 not applicable for TP53.	cspec

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