Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
Link to SEPIO compliant JSON-LD document
  • See Evidence submitted by expert panel for details.

Variant: NM_001126112.2(TP53):c.97-3C>T

CA000514

187457 (ClinVar)

Gene: TP53
Condition: Li-Fraumeni syndrome 1
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 5281b614-fb59-400c-b34d-b56faa078da3

HGVS expressions

NM_001126112.2:c.97-3C>T
NM_001126112.2(TP53):c.97-3C>T
ENST00000269305.9:c.97-3C>T
ENST00000269305.8:c.97-3C>T
ENST00000359597.8:n.97-3C>T
ENST00000413465.6:n.97-3C>T
ENST00000420246.6:c.97-3C>T
ENST00000445888.6:c.97-3C>T
ENST00000455263.6:c.97-3C>T
ENST00000503591.1:c.97-3C>T
ENST00000505014.5:n.353-3C>T
ENST00000508793.5:c.97-3C>T
ENST00000509690.5:c.-21-1039C>T
ENST00000514944.5:c.96+107C>T
ENST00000604348.5:c.97-3C>T
ENST00000610292.4:c.-21-3C>T
ENST00000610538.4:c.-21-3C>T
ENST00000615910.4:n.97-3C>T
ENST00000617185.4:c.97-3C>T
ENST00000619485.4:c.-21-3C>T
ENST00000620739.4:c.-21-3C>T
ENST00000622645.4:c.-21-3C>T
ENST00000635293.1:c.-21-3C>T
NM_000546.5:c.97-3C>T
NM_001126113.2:c.97-3C>T
NM_001126114.2:c.97-3C>T
NM_001126118.1:c.-21-3C>T
NM_001276695.1:c.-21-3C>T
NM_001276696.1:c.-21-3C>T
NM_001276760.1:c.-21-3C>T
NM_001276761.1:c.-21-3C>T
NM_001276695.2:c.-21-3C>T
NM_001276696.2:c.-21-3C>T
NM_001276760.2:c.-21-3C>T
NM_001276761.2:c.-21-3C>T
NM_000546.6:c.97-3C>T
NM_001126112.3:c.97-3C>T
NM_001126113.3:c.97-3C>T
NM_001126114.3:c.97-3C>T
NM_001126118.2:c.-21-3C>T
NM_001276695.3:c.-21-3C>T
NM_001276696.3:c.-21-3C>T
NM_001276760.3:c.-21-3C>T
NM_001276761.3:c.-21-3C>T
NC_000017.11:g.7676275G>A
CM000679.2:g.7676275G>A
NC_000017.10:g.7579593G>A
CM000679.1:g.7579593G>A
NC_000017.9:g.7520318G>A
NG_017013.2:g.16276C>T

Uncertain Significance

Met criteria codes 2
BS2_Supporting PM2_Supporting
Not Met criteria codes 14
BS4 BS3 BS1 BP2 PS1 PS2 PS4 PS3 BA1 PP1 PP3 PM6 PM5 PM1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
TP53 VCEP
This variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). This variant has been observed in 2-7 60+ year old females without a cancer diagnosis (BS2_Supporting; internal laboratory contributor). In summary, the clinical significance of TP53 c.97-3C>T is uncertain for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: PM2_Supporting, BS2_Supporting.
Met criteria codes
BS2_Supporting
Not found in FLOSSIES. Internal data (Ambry laboratories: Organization ID: 61756): one cancer-free woman 60+, Internal data (Invitae: Organization ID: 500031): three cancer-free women 60 (1) breast cancer in 60s, 2) peritoneal cancer in 60s, 3) breast cancer in 80s), (GeneDx: Organization ID: 26957): one cancer-free woman 60+. Not found in literature.
PM2_Supporting
Not found in gnomAD
Not Met criteria codes
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
varSEAK: Class 2 Likely no splicing effect. spliceAI: Acceptor Loss 0.00, Donor Loss 0.00, Acceptor Gain 0.11, Donor Gain 0.00, -22 bp
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
Not found in cancerhotspots.
Approved on: 2021-04-02
Published on: 2021-06-16
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