owencqueen/cgbench_data huggingface dataset:
Gene: FOXG1 (HGNC:3811)
Evidence Code: PM1 — Moderate
Modification Type: Disease-specific
Located in a mutational hot spot and/or critical and well-established functional domain.




Forkhead: aa 181-275
3
,
4
Gene: FOXG1 (HGNC:3811)
Evidence Code: PP3 — Supporting
Modification Type: General recommendation
Multiple lines of computational evidence support a deleterious effect on the gene or gene product.




For missense variants use REVEL with a score ≥ 0.644.


For splice site variants use SpliceAI with a score ≥ 0.2.
Gene: FOXG1 (HGNC:3811)
Evidence Code: BS3 — Strong
Modification Type: Disease-specific
Well-established in vitro or in vivo functional studies shows no damaging effect on protein function.




RNA functional studies that demonstrate no impact on splicing and transcript composition. It can be downgraded based on quality of data.


Not applicable for other functional studies.
Gene: FOXG1 (HGNC:3811)
Evidence Code: BP3 — Supporting
Modification Type: Disease-specific
In-frame deletions/insertions in a repetitive region without a known function




Inframe expansions or deletions in 
FOXG1
 repetitive regions: poly His (p.His47-p.His57), poly Gln (p.Gln70-p.Gln73) and poly Pro (p.Pro58-p.Pro61; p.Pro65-p.Pro69; p.Pro74-p.Pro80)


BP3 is applicable if there are in-frame deletions/duplications in a repetitive region where other in-frame deletions/duplications have been observed with an overall frequency commensurate with the BA1 threshold for this gene.
Gene: FOXG1 (HGNC:3811)
Evidence Code: BP4 — Supporting
Modification Type: General recommendation
For missense variants use REVEL with a score ≤ 0.290.


For splice site variants use SpliceAI with a score ≤ 0.1.
Gene: FOXG1 (HGNC:3811)
Evidence Code: BP5 — Moderate
Modification Type: Strength
Variant found in a case with an alternate molecular basis for disease.




2 cases with alternate molecular basis for disease.
Gene: FOXG1 (HGNC:3811)
Evidence Code: BP5 — Supporting
Modification Type: Disease-specific
Variant found in a case with an alternate molecular basis for disease.




1 case with alternate molecular basis for disease.
Gene: FOXG1 (HGNC:3811)
Evidence Code: BP7 — Supporting
Modification Type: None
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.




Defined 'not highly conserved' regions in BP7 as those with PhastCons score <1 and/or PhyloP score <0.1 and/or the variant is the reference nucleotide in one primate and/or three mammal species.


For splice site variants use SpliceAI with a score ≤ 0.1.