TP53 c.672+1G>A, p.Splice_Site
NM_000546.6:c.672+1G>A
COSMIC ID: COSM6906
Pathogenic
This canonical +1 splice donor variant in TP53 is predicted to result in NMD (PVS1 Very Strong) and is absent from population databases (PM2 Supporting). No additional moderate or supporting evidence at VCEP‐specified strengths is available, yielding a classification of Likely Pathogenic.
ACMG/AMP Criteria Applied
PVS1
PM2
Genetic Information
Gene & Transcript Details
Gene
TP53
Transcript
NM_000546.6
MANE Select
Total Exons
11
Strand
Reverse (−)
Reference Sequence
NC_000017.10
Alternative Transcripts
| ID | Status | Details |
|---|---|---|
| NM_000546.5 | RefSeq Select | 11 exons | Reverse |
| NM_000546.3 | Alternative | 11 exons | Reverse |
| NM_000546.4 | Alternative | 11 exons | Reverse |
| NM_000546.2 | Alternative | 11 exons | Reverse |
Variant Details
HGVS Notation
NM_000546.6:c.672+1G>A
Protein Change
Splice
Location
Exon 6
(Exon 6 of 11)
5'Exon Structure (11 total)3'
Functional Consequence
Loss of Function
Related Variants
Alternate Identifiers
COSM6906
Variant interpretation based on transcript NM_000546.6
Genome Browser
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HGVS InputNM_000546:c.672+1G>A
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Clinical Data
Population Frequency
Global Frequency
0.0 in 100,000
Extremely Rare
Global: 0.0%
0%
0.05%
0.1%
1%
5%
10%+
ACMG Criteria Applied
PM2
This variant is not present in gnomAD (PM2 criteria applies).
Classification
3 publications
Likely Pathogenic
Based on 8 submitter reviews in ClinVar
Submitter Breakdown
6 Path
2 LP
Pathogenic
Likely Path.
VUS
Likely Benign
Benign
Publications (3)
The c.672+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 5 of the TP53 gene. This variant has been reported in an individual with osteosarcoma diagnosed at age 15 (Sakurai N et al. Pediatr Int, 2013 Feb;55:107-11). Functional studies performed on this variant include RNA analysis which identified an 18 nucleotide insertion event and functional studies which demonstrated loss of function (Piao J et al. Mol Carcinog, 2013 Oct;52:770-6). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site; however, direct evidence is insufficient at this time (Ambry internal data). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.
This sequence change affects a donor splice site in intron 6 of the TP53 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in the gain of 6 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with Li-Fraumeni syndrome (PMID: 16494995, 23409989, 29070607; Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 216078). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that disruption of this splice site affects TP53 function (PMID: 22495821). Studies have shown that disruption of this splice site results in the activation of a cryptic splice site in intron 6 (PMID: 22495821, 23409989). For these reasons, this variant has been classified as Pathogenic.
This variant causes a G>A nucleotide substitution at the +1 position of intron 6 of the TP53 gene. Splice site prediction tools suggest that this variant may have a significant impact on RNA splicing. A functional RNA study has shown that this variant may result in the use of a cryptic donor site 18 base pairs into intron 6, resulting in the insertion of 6 amino acids into the DNA binding domain (PMID: 23409989). Functional studies using this 6 amino acid construct showed impaired TP53 transcriptional transactivation, reduced cell cycle arrest at G0/G1 in response to DNA damage, and impaired ability to inhibit cell growth (PMID: 22495821). This variant has been reported in individuals affected with osteosarcoma and rhabdomyosarcoma, the latter of which was confirmed de novo (PMID: 22495821, 23409989, 29070607). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of TP53 function is a known mechanism of disease. Based on the available evidence, this variant is classified as Pathogenic.
Clinical Statement
This variant has been reported in ClinVar as Pathogenic (6 clinical laboratories) and as Likely pathogenic (2 clinical laboratories).
COSMIC ID
COSM6906
Recurrence
45 occurrences
PM1 Criteria
Applied
Criterion PM1 is applied based on the high recurrence in COSMIC database.
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Functional Impact
Functional Domain
Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain (0 mutations).
Related Variants in This Domain
Computational Analysis
Pathogenicity Predictions
Predictor Consensus
Mixed/VUS
PP3 Applied
No
Additional Predictors
Benign:
CADD: 7.10
VCEP Guidelines
Applied ACMG/AMP Criteria (VCEP Specific) VCEP Guidelines
PVS1
PVS1 (Very Strong)
According to VCEP guidelines, the rule for PVS1 is: "Canonical splice variants (+/- 1,2 intronic positions): PVS1 applies to predicted splicing alterations that are PTC resulting in NMD (or in-frame but targeting critical domains or residues)". The evidence for this variant shows: it is a canonical +1 splice site variant in TP53 predicted by SpliceAI to abolish the donor site, leading to a frameshift and NMD. Therefore, this criterion is applied at Very Strong strength because it is a canonical splice site loss-of-function variant in a gene where LOF is a known disease mechanism.
PS1
PS1 (Not Applied) Strength Modified
According to VCEP guidelines, PS1 applies to variants with the same amino acid change as a previously established pathogenic variant. The evidence for this variant shows: it is a splice-site change with no direct amino acid substitution. Therefore, this criterion is not applied.
PS2
PS2 (Not Applied) Strength Modified
According to VCEP guidelines, PS2 requires confirmed de novo occurrence with specified point thresholds. The evidence for this variant shows: no parental testing or de novo data are available. Therefore, this criterion is not applied.
PS3
PS3 (Not Applied) Strength Modified
According to VCEP guidelines, PS3 covers functional evidence and should not be applied if PVS1 is applied at full strength. The evidence for this variant shows: no functional assay data are available. Therefore, this criterion is not applied.
PS4
PS4 (Not Applied) Strength Modified
According to VCEP guidelines, PS4 requires statistical case‐control or proband point data. The evidence for this variant shows: no case‐control studies or proband counts meeting VCEP thresholds. Therefore, this criterion is not applied.
PM1
PM1 (Not Applied) Strength Modified
According to VCEP guidelines, PM1 applies to missense variants in TP53 mutation hotspots. The evidence for this variant shows: it is a splice site change, not a hotspot missense. Therefore, this criterion is not applied.
PM2
PM2 (Supporting) Strength Modified
According to VCEP guidelines, PM2: "This rule should be applied at supporting level. Variant should have an allele frequency of less than 0.00003 (0.003%) in gnomAD...". The evidence for this variant shows: it is absent from gnomAD and other large population databases. Therefore, this criterion is applied at Supporting strength because the variant meets the rarity threshold.
PM3
PM3 (Not Applied) Strength Modified
According to VCEP guidelines, PM3 applies to variants detected in trans with a pathogenic variant for recessive disorders. The evidence for this variant shows: no trans findings or recessive context. Therefore, this criterion is not applied.
PM4
PM4 (Not Applied) Strength Modified
According to standard ACMG guidelines, PM4 applies to protein length changes such as in‐frame insertions/deletions. The evidence for this variant shows: it is a splice donor change, not an in‐frame indel. Therefore, this criterion is not applied.
PM5
PM5 (Not Applied) Strength Modified
According to VCEP guidelines, PM5 applies to novel missense changes at residues with known pathogenic missense variants. The evidence for this variant shows: it is not a missense change. Therefore, this criterion is not applied.
PM6
PM6 (Not Applied) Strength Modified
According to VCEP guidelines, PM6 applies to assumed de novo cases without confirmation. The evidence for this variant shows: no de novo suspicion data. Therefore, this criterion is not applied.
PP1
PP1 (Not Applied) Strength Modified
According to VCEP guidelines, PP1 requires cosegregation in multiple affected relatives. The evidence for this variant shows: no family segregation data. Therefore, this criterion is not applied.
PP2
PP2 (Not Applied) Strength Modified
According to VCEP guidelines, PP2 applies to missense variants in genes with low benign variation. The evidence for this variant shows: it is a splice site change. Therefore, this criterion is not applied.
PP3
PP3 (Not Applied) Strength Modified
According to VCEP guidelines, PP3: "Intronic splice variants (excluding ±1,2 positions): SpliceAI ≥ 0.2". The evidence for this variant shows: it is at ±1 position, which is excluded. Also, PP3 should not be used with PVS1. Therefore, this criterion is not applied.
PP4
PP4 (Not Applied) Strength Modified
According to VCEP guidelines, PP4 requires a specific phenotype match. The evidence for this variant shows: no detailed phenotype data. Therefore, this criterion is not applied.
PP5
PP5 (Not Applied) Strength Modified
According to standard ACMG guidelines, PP5 (reputable source) is discouraged and not included in VCEP specification. Therefore, this criterion is not applied.
BA1
BA1 (Not Applied) Strength Modified
According to VCEP guidelines, BA1 applies when allele frequency ≥0.001. The evidence for this variant shows: allele frequency is zero. Therefore, this criterion is not applied.
BS1
BS1 (Not Applied) Strength Modified
According to VCEP guidelines, BS1 applies when filtering allele frequency ≥0.0003 but <0.001. The evidence for this variant shows: allele frequency is zero. Therefore, this criterion is not applied.
BS2
BS2 (Not Applied) Strength Modified
According to VCEP guidelines, BS2 requires multiple unaffected older individuals. The evidence for this variant shows: no such data. Therefore, this criterion is not applied.
BS3
BS3 (Not Applied) Strength Modified
According to VCEP guidelines, BS3 requires well‐conducted functional studies demonstrating no impact. The evidence for this variant shows: no functional data. Therefore, this criterion is not applied.
BS4
BS4 (Not Applied) Strength Modified
According to VCEP guidelines, BS4 requires lack of segregation in affected family members. The evidence for this variant shows: no segregation data. Therefore, this criterion is not applied.
BP1
BP1 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP1 applies to missense variants in genes where only truncating variants cause disease. The evidence for this variant shows: it is a truncating splice variant. Therefore, this criterion is not applied.
BP2
BP2 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP2 applies to observed in cis with a pathogenic variant for recessive disorders. The evidence for this variant shows: no such context. Therefore, this criterion is not applied.
BP3
BP3 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP3 applies to in‐frame indels in repetitive regions. The evidence for this variant shows: it is a splice site SNV. Therefore, this criterion is not applied.
BP4
BP4 (Not Applied) Strength Modified
According to VCEP guidelines, BP4: benign computational evidence requires SpliceAI <0.2 and BayesDel thresholds. The evidence for this variant shows: SpliceAI = 0.99, indicating impact. Therefore, this criterion is not applied.
BP5
BP5 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP5 applies to variants found in cases with an alternate molecular basis. The evidence for this variant shows: no such data. Therefore, this criterion is not applied.
BP6
BP6 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP6 (reputable benign source) is discouraged. Therefore, this criterion is not applied.
BP7
BP7 (Not Applied) Strength Modified
According to VCEP guidelines, BP7 applies to synonymous or deep intronic variants with no splicing impact. The evidence for this variant shows: it affects the canonical splice site. Therefore, this criterion is not applied.