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]
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  • See Evidence submitted by expert panel for details.

Variant: NM_000314.6(PTEN):c.1027-1G>A

CA16042723

372482 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 1efc38fb-30b6-43c9-b8d5-0f1836b4fb0e

HGVS expressions

NM_000314.6:c.1027-1G>A
NM_000314.6(PTEN):c.1027-1G>A
NC_000010.11:g.87965286G>A
CM000672.2:g.87965286G>A
NC_000010.10:g.89725043G>A
CM000672.1:g.89725043G>A
NC_000010.9:g.89715023G>A
NG_007466.2:g.106848G>A
NM_000314.5:c.1027-1G>A
NM_001304717.2:c.1546-1G>A
NM_001304718.1:c.436-1G>A
NM_000314.7:c.1027-1G>A
NM_001304717.5:c.1546-1G>A
NM_001304718.2:c.436-1G>A
ENST00000371953.7:c.1027-1G>A

Pathogenic

Met criteria codes 3
PM6 PM2 PVS1
Not Met criteria codes 18
BP7 BP5 BP4 BP2 BA1 PP2 PP1 PM5 PM4 PM1 BS1 BS3 BS4 BS2 PS2 PS1 PS4 PS3

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.1027-1G>A (IVS8-1G>A) meets criteria to be classified as pathogenic 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). PVS1: Null variant predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5’ to c.1121 (NM_000314.4). PM2: Absent in large sequenced populations (PMID 27535533). PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (Internal laboratory contributor SCV000490754.2)
Met criteria codes
PM6
1 GDx internal case. FH - I agree
PM2
absent gnomAD (I agree - FH)
PVS1
I agree (FH)
Not Met criteria codes
BP7
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
BP4
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
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
Variant present in proband, 6yo F with thyroid nodules and macrocephaly, and her father with goiter and lipoma. Is also GDx internal family. 1 meiosis. PubMed:20962022
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
BS1
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
Variant present in proband, 6yo F with thyroid nodules and macrocephaly, and her father with goiter and lipoma. Is also GDx internal family. 1 meiosis. PubMed:20962022
BS2
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
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
variant reported in 41yo M with "CS" - pts from CCF cohort. no other phenotype provided. PubMed:27477328
Variant present in proband, 6yo F with thyroid nodules and macrocephaly, and her father with goiter and lipoma. Is also GDx internal family. 0.5 phenotype points. PubMed:20962022
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2019-06-25
Published on: 2019-07-23
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