owencqueen/cgbench_data huggingface dataset:
Gene: PTEN (HGNC:9588)
Evidence Code: PVS1 — Very Strong
Modification Type: Disease-specific
Use PTEN PVS1 decision tree.
Gene: PTEN (HGNC:9588)
Evidence Code: PVS1 — Strong
Modification Type: Disease-specific
Use PTEN PVS1 decision tree.
Gene: PTEN (HGNC:9588)
Evidence Code: PVS1 — Moderate
Modification Type: Disease-specific
Use PTEN PVS1 decision tree.
Gene: PTEN (HGNC:9588)
Evidence Code: PS3 — Strong
Modification Type: Disease-specific
Well-established 
in vitro
 or 
in vivo
 functional studies supportive of a damaging effect on the gene or gene product.




RNA, mini-gene, or other assay shows impact on splicing
Gene: PTEN (HGNC:9588)
Evidence Code: PS3 — Moderate
Modification Type: Disease-specific
Well-established 
in vitro
 or 
in vivo
 functional studies supportive of a damaging effect on the gene or gene product.




Phosphatase activity ≤ -1.11 per Mighell et al. 2018, PMID: 29706350.
Gene: PTEN (HGNC:9588)
Evidence Code: PS3 — Supporting
Modification Type: Disease-specific,Strength
Phosphatase activity <50% of wild-type or abnormal 
in vitro
 cellular assay or transgenic model with phenotype different from wild type that does not meet PS3_moderate.
Gene: PTEN (HGNC:9588)
Evidence Code: PM2 — Supporting
Modification Type: Disease-specific
Absent in population




Databases present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population.  If multiple alleles are present within any subpopulation, allele frequency in that subpopulation must be <0.00002 (0.002%).
Gene: PTEN (HGNC:9588)
Evidence Code: PM4 — Moderate
Modification Type: Disease-specific
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. Applies to in-frame insertions or deletions impacting at least one residue in a catalytic motif (see PM1), and variants causing protein extension.
Gene: PTEN (HGNC:9588)
Evidence Code: PM6 — Strong
Modification Type: Strength
Two probands with presumed 
de novo
 occurrence (maternity/ paternity not confirmed) with the disease and no family history.




May also be used for a proband with presumed de novo occurrence for an individual with a highly specific phenotype (meets criteria to count towards PS4)
Gene: PTEN (HGNC:9588)
Evidence Code: PP3 — Supporting
Modification Type: Disease-specific
Multiple lines of computational evidence support a deleterious effect on the gene or gene product.




Splicing variants: Concordance of SpliceAl and VarSeak


Missense variants: REVEL score > 0.7
Gene: PTEN (HGNC:9588)
Evidence Code: BA1 — Stand Alone
Modification Type: Disease-specific
gnomAD Filtering allele frequency >0.00056 (0.056%)
Gene: PTEN (HGNC:9588)
Evidence Code: BS1 — Strong
Modification Type: Disease-specific
gnomAD Filtering allele frequency from 0.000043 (0.0043%) up to 0.00056 (0.056%)
Gene: PTEN (HGNC:9588)
Evidence Code: BS1 — Supporting
Modification Type: Disease-specific,Strength
Allele frequency from 0.0000043 (0.00043%) up to 0.000043 (0.0043%).
Gene: PTEN (HGNC:9588)
Evidence Code: BS3 — Strong
Modification Type: Disease-specific
Well-established 
in vitro
 or 
in vivo
 functional studies shows no damaging effect on protein function. To be applied to intronic or synonymous variants, RNA, mini-gene or other splicing assay demonstrating no splicing impact.
Gene: PTEN (HGNC:9588)
Evidence Code: BS3 — Supporting
Modification Type: Disease-specific,Strength
In vitro
 or 
in vivo
 functional study or studies showing no damaging effect on protein function.




Phosphatase activity >0 per Mighell et al. 2018, PMID: 29706350.
Gene: PTEN (HGNC:9588)
Evidence Code: BP4 — Supporting
Modification Type: Disease-specific
Multiple lines of computational evidence suggest no impact on gene or gene product. 




Splicing variants: Concordance of SpliceAl and VarSeak


Missense variants: REVEL scores < 0.5
Gene: PTEN (HGNC:9588)
Evidence Code: BP7 — Supporting
Modification Type: Disease-specific
A synonymous (silent) or intronic variant at or beyond +7/-21 for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice.