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]
  • See Evidence submitted by expert panel for details.

Variant: NM_000314.7(PTEN):c.720C>T (p.Tyr240=)

CA000191

183876 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 46a0658f-d1ec-44af-8a4b-2a05b09dd6b3
Approved on: 2019-11-22
Published on: 2019-12-11

HGVS expressions

NM_000314.7:c.720C>T
NM_000314.7(PTEN):c.720C>T (p.Tyr240=)
NC_000010.11:g.87957938C>T
CM000672.2:g.87957938C>T
NC_000010.10:g.89717695C>T
CM000672.1:g.89717695C>T
NC_000010.9:g.89707675C>T
NG_007466.2:g.99500C>T
NM_000314.5:c.720C>T
NM_000314.6:c.720C>T
NM_001304717.2:c.1239C>T
NM_001304718.1:c.129C>T
NM_001304717.5:c.1239C>T
NM_001304718.2:c.129C>T
ENST00000371953.7:c.720C>T
ENST00000472832.2:n.147C>T
More

Likely Benign

Met criteria codes 3
BS1_Supporting BP7 BP4
Not Met criteria codes 19
PP2 PP3 PP1 PM2 PM6 PM5 PM4 PM1 PVS1 BA1 BS2 BS3 BS4 BP5 BP2 PS1 PS3 PS4 PS2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.720C>T (p.Tyr240=) meets criteria to be classified as likely benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). BP4: Synonymous variant where at least 2 out of 3 in silico models predict no splicing impact. BP7: Variant is synonymous (silent), nucleotide is not conserved, and no splicing impact is predicted. BS1_P: Allele frequency of 0.00010 (0.010%, 13/129,168 alleles) in the European (non-Finnish) subpopulation of the gnomAD cohort. (PMID 27535533)
Met criteria codes
BS1_Supporting
0.01% European; 13/129,168 alleles
BP7
No new splice site predicted, and variant is not highly conserved.
BP4
The in silico tools of MaxEnt, NNS, and HSF show no difference between wildtype and variant (values = 0%).
Not Met criteria codes
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
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
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
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
BS2
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
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
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
PS3
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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