Variant classification summary

NM_000546.6:c.716A>G

TP53 · NP_000537.3:p.(Asn239Ser) · NM_000546.6

GRCh37: chr17:7577565 T>C · GRCh38: chr17:7674247 T>C

Gene: TP53 Transcript: NM_000546.6

Final call

Likely Pathogenic

PS3 strong PM2 supporting PM5 strong BP4 supporting benign

Variant details

Gene

TP53

Transcript

NM_000546.6

Protein

NP_000537.3:p.(Asn239Ser)

gnomAD AF

6.196201480644306e-07 (v4.1)

ClinVar

Likely pathogenic

OncoKB

Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

PS3_Strong is met (+4 points): N239S is non-functional in the Kato et al. functional assay and shows loss of function in all three other eligible VCEP assays (Giacomelli, Kotler, Funk), meeting the TP53 VCEP criterion for strong pathogenic functional evidence.

2

PM5_Strong is met (+4 points): At codon 239, three different missense variants (N239D, N239I, N239T) have been classified as pathogenic (PS3) by the TP53 VCEP, satisfying the requirement of ≥2 different pathogenic missense variants at the same residue.

3

PM2_Supporting is met (+1 point): The variant is extremely rare in population databases (gnomAD v4.1 AF = 6.2e-7), well below the VCEP threshold of <0.00003.

4

BP4_Supporting is met (-1 point): Per the VCEP PP3-BP4-codes.xlsx, c.716A>G is assigned BP4. BayesDel score 0.10537 with aGVGD Class C45 and no predicted splicing impact (SpliceAI 0.04).

5

Tavtigian point total: 4 (PS3) + 4 (PM5) + 1 (PM2) - 1 (BP4) = 8 points. Under the TP53 VCEP v2.4.0 point-based framework, 6-9 points corresponds to Likely Pathogenic.

6

The variant has been observed in ClinVar with majority classification as Likely Pathogenic (6 clinical laboratories) and Pathogenic (1 laboratory), consistent with this adjudication.

7

N239S has been reported as a somatic mutation in 56 tumor samples in COSMIC and is classified as Oncogenic (Loss-of-function) by OncoKB, though these somatic data are not directly used for germline criterion points under the VCEP framework.

Final determination: Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework yields a total score of 8, 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. The TP53 VCEP PVS1 flowchart applies only to null variants (nonsense, frameshift, canonical ±1,2 splice site, initiation codon, and exon-level deletions). NM_000546.6:c.716A>G is a missense substitution (p.Asn239Ser).	vcep_pvs1_flowchart
PS1	N/A	PS1 requires a different nucleotide change yielding the same amino acid change that has been previously classified as pathogenic by the TP53 VCEP. NM_000546.6:c.716A>G (p.Asn239Ser) represents a single nucleotide substitution; no alternative nucleotide change at this position yields the same amino acid change (N239S).	cspec
PS2	Not assessed	No de novo observation of NM_000546.6:c.716A>G (p.Asn239Ser) with confirmed paternity and maternity was identified in the literature, ClinVar, or published databases reviewed. De novo status cannot be determined from available evidence.
PS3	Met	N239S is classified as PS3 by the TP53 VCEP Functional-worksheet (Supplementary Table S3). In the Kato et al. (PMID:12826609) functional assay, N239S is non-functional. In the three other eligible VCEP assays, N239S shows loss of function: Giacomelli (PMID:30224644): LOF; Kotler (PMID:29979965): LOF; Funk (PMID:39774325): LOF. This meets the VCEP PS3_Strong criteria: non-functional on Kato data AND loss of function by the majority of other eligible assays (3/3 LOF).	vcep_functional_worksheet PMID:12826609
PS4	Not assessed	Although the PM2_Supporting prerequisite is satisfied (variant is extremely rare in population databases), no proband-level cancer phenotype data or case-control analysis is available to calculate Li-Fraumeni syndrome cancer points under the TP53 VCEP PS4 scoring system. The variant has 56 somatic observations in COSMIC and is listed as Oncogenic in OncoKB, but these somatic data alone do not meet the VCEP PS4 proband-based point thresholds.	gnomad_v4 oncokb
PS5	N/A	PS5 is not included in the TP53 VCEP v2.4.0 criteria specification. The same-residue different-missense-change scenario is addressed in this framework by the PM5 criterion, which has VCEP-specific strength rules.	cspec
PM1	Not met	Codon 239 is not among the VCEP-designated PM1 hotspot codons (175, 245, 248, 249, 273, 282). The exact variant (N239S) is not listed as a standalone entry in cancerhotspots.org with ≥10 somatic occurrences (exact_variant_listed: no), though the residue lies in a statistically significant hotspot and COSMIC reports 56 somatic occurrences for this variant. Under the VCEP PM1 rules, neither codon-based nor cancerhotspots-based thresholds are met.	cspec
PM2	Met	The variant is extremely rare in population databases. In gnomAD v4.1, the global allele frequency is 6.20e-7 (1 allele / 1,613,892 alleles; 0.000062%), with the only allele observed in the European (non-Finnish) subpopulation (AF = 8.48e-7; 1/1,179,928 alleles). This is well below the VCEP PM2_Supporting threshold of <0.00003 (0.003%). The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0. No homozygotes observed.	gnomad_v4 gnomad_v2 gnomad_canada
PM5	Met	At codon 239, at least three different missense variants (N239D, N239I, N239T) have been independently classified as PS3 (Pathogenic) by the TP53 VCEP Functional-worksheet. This satisfies PM5_Strong: ≥2 different missense variants at the same amino acid residue previously determined to be pathogenic per TP53 VCEP specifications.	vcep_functional_worksheet
PM6	N/A	Skipped per adjudication directive. PM6 is not applicable per TP53 VCEP specifications.
PP1	Not assessed	No cosegregation data identified for NM_000546.6:c.716A>G. No published pedigrees or family studies reporting segregation of this variant with Li-Fraumeni syndrome or TP53-associated cancers were found.
PP2	N/A	PP2 is not applicable per TP53 VCEP v2.4.0 specifications.	cspec
PP3	Not met	Per the TP53 VCEP PP3-BP4-codes.xlsx (Supplementary Table S2), c.716A>G (p.Asn239Ser) is assigned BP4, not PP3. The variant has BayesDel score 0.10537 (aGVGD Class C45), which is below the 0.16 threshold for PP3_Supporting. SpliceAI max delta = 0.04, indicating no predicted splicing effect (<0.2). Per the VCEP PP3/BP4 flowchart, aGVGD Class C45 with BayesDel <0.16 and no predicted splicing effect meets BP4, not PP3.	vcep_pp3_bp4_codes bayesdel spliceai
PP4	Not assessed	The TP53 VCEP PP4 criterion requires variant allele fraction (VAF) data from clinical testing to distinguish constitutional from somatic/clonal hematopoiesis origin. No VAF data or clinical phenotype information is available in the evidence reviewed.
PP5	N/A	PP5 is not for use per the TP53 VCEP v2.4.0 specifications, as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BA1	Not met	The variant is extremely rare in gnomAD v4.1 (global AF = 6.2e-7). No continental subpopulation has a filtering allele frequency (FAF) ≥0.001 (0.1%). The VCEP BA1 stand-alone benign threshold is not approached.	gnomad_v4
BS1	Not met	The variant is extremely rare in gnomAD v4.1 (global AF = 6.2e-7). No continental subpopulation has an allele frequency ≥0.0003 (0.03%). The VCEP BS1 strong benign threshold is not approached.	gnomad_v4
BS2	Not assessed	No data available on unrelated females aged ≥60 years without cancer who carry this variant. BS2 requires a minimum of 2 such individuals from a single source, which has not been identified.
BS3	Not met	N239S is non-functional in the Kato et al. assay (PMID:12826609) and shows loss of function in all other eligible VCEP assays (Giacomelli, Kotler, Funk). The VCEP Functional-worksheet assigns PS3, not BS3. BS3 requires the variant to be functional or partially functional on Kato data with no LOF by the majority of available assays, which is contradicted by the non-functional Kato result and uniform LOF across supporting assays.	vcep_functional_worksheet
BS4	Not assessed	No evidence of lack of segregation identified. No reports of this variant in unaffected family members of Li-Fraumeni syndrome families, nor observations in healthy elderly controls, were found in the literature or databases reviewed.
BP1	N/A	BP1 is not applicable per TP53 VCEP v2.4.0 specifications. The VCEP states this rule does not apply to TP53 as truncating variants account for only a portion of disease-causing variants.	cspec
BP2	N/A	BP2 is not applicable per TP53 VCEP v2.4.0 specifications.	cspec
BP3	N/A	Skipped per adjudication directive. In-frame deletion/insertion in repetitive region; not applicable to this missense substitution.
BP4	Met	Per the TP53 VCEP PP3-BP4-codes.xlsx (Supplementary Table S2), c.716A>G (p.Asn239Ser) is assigned BP4. The variant has BayesDel score 0.10537, which is <0.16 and >-0.008, with aGVGD Class C45 (not C65). SpliceAI max delta = 0.04, indicating no predicted splicing effect (<0.2). This meets the VCEP BP4_Supporting criteria: BayesDel <0.16 and >-0.008 (excluding C65) AND no predicted differences in splicing (SpliceAI <0.2).	vcep_pp3_bp4_codes bayesdel spliceai
BP5	N/A	BP5 is not applicable per TP53 VCEP v2.4.0 specifications.	cspec
BP6	N/A	BP6 is not applicable per TP53 VCEP v2.4.0 specifications.	cspec
BP7	N/A	BP7 applies only to synonymous (silent) or intronic variants. NM_000546.6:c.716A>G is a missense variant and does not qualify for BP7 assessment.	cspec

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