Variant classification summary

NM_000546.6:c.-29+121G>T

TP53 · NP_000537.3:p.? · NM_000546.6

GRCh37: chr17:7590574 C>A · GRCh38: chr17:7687256 C>A

Gene: TP53 Transcript: NM_000546.6

Final call

VUS

PM2 supporting BP4 supporting benign BP7 supporting benign

Variant details

Gene

TP53

Transcript

NM_000546.6

Protein

NP_000537.3:p.?

gnomAD AF

ClinVar

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000546.6:c.-29+121G>T is a deep intronic substitution in intron 1 of TP53, 121 nucleotides downstream of the exon 1 splice donor (c.-29). This variant falls outside all canonical null-variant categories (PVS1 not applicable) and does not alter the amino acid sequence (PS1, PM1, PM5 not applicable).

2

The variant is absent from gnomAD v2.1 and v4.1 (0 alleles across >1.6 million individuals). This absence meets the TP53 VCEP PM2_Supporting threshold of allele frequency < 0.00003 (0.003%). However, caution is warranted as deep intronic regions may have reduced coverage in exome sequencing data.

3

SpliceAI predicts no splicing impact (max delta score = 0.00). No cryptic splice site creation or disruption is predicted. This supports a benign interpretation through two independent TP53 VCEP criteria: BP4_Supporting (computational evidence, SpliceAI ≤ 0.1 for intronic variants outside ±1,2) and BP7_Supporting (intronic variant at +121, beyond +7, with no predicted splicing aberration).

4

No functional studies, de novo observations, co-segregation data, case-control studies, or ClinVar submissions have been reported for this variant. It is absent from COSMIC and all TP53 locus-specific databases. Multiple pathogenic criteria (PS2, PS3, PS4, PP1, PP4) and benign criteria (BS1, BS2, BS3, BS4, BA1) cannot be assessed due to complete absence of variant-specific clinical or experimental data.

5

Under the TP53 VCEP v2.4.0 Tavtigian point-based framework, the applied criteria yield: PM2_Supporting (+1 point), BP4_Supporting (-1 point), BP7_Supporting (-1 point). Total = -1 point, which maps to Uncertain Significance (range -1 to +5). However, the VCEP caveat states that a final point value of -1 may be overridden to Likely Benign when at least 2 benign evidence codes are applied AND PM2_Supporting is the only pathogenic code. Both conditions are met here, resulting in a final classification of Likely Benign.

Final determination: Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework yields a total score of -1, 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 reserved for null variants (nonsense, frameshift, canonical ±1,2 splice sites, initiation codon, exon deletions) in TP53. NM_000546.6:c.-29+121G>T is a deep intronic substitution at position +121 in intron 1, which does not fall into any PVS1 null-variant bucket. SpliceAI predicts no splicing impact (max delta = 0.00). Not applicable per TP53 VCEP PVS1 flowchart.	pvs1_variant_assessment pvs1_gene_context spliceai
PS1	N/A	PS1 applies to variants producing the same amino acid change as a previously established P/LP variant per TP53 VCEP specifications. NM_000546.6:c.-29+121G>T is an intronic variant that does not alter the amino acid sequence. No protein change to compare.
PS2	Not met	No de novo observations of NM_000546.6:c.-29+121G>T have been reported in probands with Li-Fraumeni syndrome or TP53-associated cancers. Variant is absent from ClinVar, published literature, and clinical testing databases. Zero proband points available per TP53 VCEP PS2 scoring table.	clinvar
PS3	Not met	No functional studies have been performed on NM_000546.6:c.-29+121G>T. The TP53 VCEP functional worksheet (Supplementary Table S3) covers missense amino acid substitutions and in-frame deletions only; this deep intronic variant is outside the scope of eligible functional assays (Kato, Giacomelli, Kotler, Funk, Kawaguchi). No variant-specific functional data exist.
PS4	Not met	No observations of NM_000546.6:c.-29+121G>T have been reported in affected individuals. The variant is absent from ClinVar, COSMIC, and gnomAD. No proband data are available to tally points under the TP53 VCEP PS4 cancer scoring table. Zero points = PS4 not met.	clinvar gnomad_v2 gnomad_v4 gnomad_canada
PS5	N/A	Not assessed per instruction.
PM1	N/A	PM1 applies to missense variants at TP53 hotspot codons (175, 245, 248, 249, 273, 282) or with ≥2 somatic occurrences at cancerhotspots.org for the same amino acid change. NM_000546.6:c.-29+121G>T is an intronic substitution, not a missense variant. No amino acid residue is affected.
PM2	Met	NM_000546.6:c.-29+121G>T is absent from gnomAD v2.1 and v4.1 (0 alleles). This meets the TP53 VCEP PM2_Supporting threshold of allele frequency < 0.00003 (0.003%). Caveat: deep intronic positions may have reduced coverage in exome sequencing data, which may contribute to apparent absence.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	PM5 applies to missense variants at an amino acid residue where a different P/LP missense change has been established per TP53 VCEP specifications. NM_000546.6:c.-29+121G>T is an intronic variant that does not alter the amino acid sequence.	pm5_candidates
PM6	N/A	The TP53 VCEP combines PS2 and PM6 under a unified de novo scoring system; PM6 as a standalone criterion is not applicable per the VCEP specifications. De novo assessment is addressed under PS2.
PP1	Not met	No co-segregation data available for NM_000546.6:c.-29+121G>T. No families with this variant have been reported. Zero meioses observed = PP1 not met per TP53 VCEP thresholds (Supporting requires 3-4 meioses).
PP2	N/A	PP2 is not applicable per TP53 VCEP specifications.
PP3	Not met	For intronic variants outside ±1,2 splice positions, TP53 VCEP PP3_Supporting requires SpliceAI ≥ 0.2. SpliceAI max delta for NM_000546.6:c.-29+121G>T is 0.00, well below the threshold. No predicted splice-altering effect. PP3 is not met.	spliceai
PP4	Not met	No observations of NM_000546.6:c.-29+121G>T with variant allele fraction (VAF) 5-35% have been reported. The variant is absent from all databases. Zero qualifying observations = PP4 not met per TP53 VCEP specifications.	clinvar
PP5	N/A	PP5 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee per TP53 VCEP v2.4.0.
BA1	Not met	NM_000546.6:c.-29+121G>T is absent from gnomAD (0 alleles in v2.1 and v4.1). BA1 requires filtering allele frequency (FAF) ≥ 0.001 (0.1%) in a continental subpopulation. Frequency of 0 is well below this threshold.	gnomad_v2 gnomad_v4
BS1	Not met	NM_000546.6:c.-29+121G>T is absent from gnomAD (0 alleles). BS1 requires FAF ≥ 0.0003 (0.03%) but < 0.001 in a continental subpopulation. Frequency of 0 does not meet the lower bound.	gnomad_v2 gnomad_v4
BS2	Not met	No observations of NM_000546.6:c.-29+121G>T in unaffected females ≥60 years without cancer have been reported. Zero qualifying individuals = BS2 not met per TP53 VCEP specifications (Supporting requires at least 2-3 such individuals from a single source).
BS3	Not met	No functional studies demonstrating a benign effect for NM_000546.6:c.-29+121G>T have been performed. The TP53 VCEP functional assay panel (Kato, Giacomelli, Kotler, Funk, Kawaguchi) covers missense amino acid changes and small in-frame deletions only. This deep intronic variant is outside the scope of eligible functional assays.
BS4	Not met	No segregation data demonstrating lack of co-segregation with LFS-associated cancers have been reported for NM_000546.6:c.-29+121G>T. No family studies available.
BP1	N/A	BP1 is not applicable per TP53 VCEP specifications. This rule code does not apply to TP53 as truncating variants account for only a portion of disease-causing variants.
BP2	N/A	BP2 is not applicable per TP53 VCEP specifications.
BP4	Met	NM_000546.6:c.-29+121G>T is an intronic variant outside ±1,2 splice positions with SpliceAI max delta = 0.00. Per TP53 VCEP BP4 rules, intronic variants outside ±1,2 positions with SpliceAI ≤ 0.1 meet BP4_Supporting.	spliceai
BP5	N/A	BP5 is not applicable per TP53 VCEP specifications.
BP6	N/A	BP6 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee per TP53 VCEP v2.4.0.
BP7	Met	NM_000546.6:c.-29+121G>T is an intronic variant at position +121 (beyond +7 from the splice donor) with SpliceAI max delta = 0.00, predicting no impact on splicing. Per TP53 VCEP BP7_Supporting rule: intronic variants at or beyond +7 to -21 positions with SpliceAI ≤ 0.1 and BP4 met qualify for BP7_Supporting.	spliceai
BP3	N/A	In-frame deletions/insertions in repetitive region without known function. Not applicable: this is a single nucleotide substitution, not an in-frame indel.
PM3	N/A	Recessive disorder criterion. Not applicable to TP53/Li-Fraumeni syndrome (autosomal dominant).
PM4	N/A	Protein length change criterion. Not applicable: this is a single nucleotide substitution, not an in-frame deletion/insertion or stop-loss variant.

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