Associated Phenotype Example Modeling

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O
1	id	value	method	component:gene-studied	component:amino-acid-chg	component:variant-consequence	component:functional-effect	component:genomic-dna-chg	component:sample-allelic-frequency	component:allelic-state	component:genomic-source-class	component:copy-number	extension:SecondaryFinding	note	report

2	PTEN	Present	Sequencing	PTEN	p.Y68fs	SO:0001589#frameshift_variant;	SO:0002054#LOF;SO:0001786#LOH	NM_000314:c.203_207del	17.80%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
3	KRAS	Present	Sequencing	KRAS	p.G12D	Missense variant (exon 2)	SO:0002053#GOF	NM_033360:c.35G>A	15.80%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
4	APC1	Present	Sequencing	APC	p.Q1444*	SO:0001587#stop gain	SO:0002054#LOF	NM_000038:c.4330C>T	15.50%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
5	FAT1	Present	Sequencing	FAT1	p.E992*	SO:0001587#stop gain	SO:0002054#LOF	NM_005245:c.2974G>T	14.90%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
6	CHEK2	Present	Sequencing	CHEK2	p.R145W	SO:0001583#Missense variant		NM_007194:c.433C>T		Heterozygous	Germline		acmg-version1		https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
7	LMO1	Present	Sequencing	LMO1	p.L118I	SO:0001583#Missense variant		NM_002315:c.352C>A	18.20%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
8	APC2	Present	Sequencing	APC	p.P1439S	SO:0001583#Missense variant		NM_000038:c.4315C>T	14.70%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
9	LRP1B	Present	Sequencing	LRP1B	p.E3A	SO:0001583#Missense variant		NM_018557:c.8A>C	14.60%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
10	KAT6A	Present	Sequencing	KAT6A	p.M1884I	SO:0001583#Missense variant		NM_006766:c.5652G>T	13.50%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
11	ATIC	Present	Sequencing	ATIC	p.H584N	SO:0001583#Missense variant		NM_004044:c.1750C>A	11.50%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
12	MAP2K2	Present	Sequencing	MAP2K2	p.R313W	SO:0001583#Missense variant		NM_030662:c.937C>T	11.00%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
13	MYH11	Present	Sequencing	MYH11	p.R108W	SO:0001583#Missense variant		NM_002474:c.322C>T	10.10%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
14	RICTOR	Present	Sequencing	RICTOR	p.K678T	SO:0001583#Missense variant		NM_001285439:c.2033A>C	9.10%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
15	DPYD	Present	Sequencing	DPYD	p.R74Q	SO:0001583#Missense variant		NM_000110:c.221G>A	7.60%		Somatic				https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
16	BRAF	Absent	Sequencing	BRAF;NRAS										No pathogenic single nucleotide variants, indels, or copy number changes were found in BRAF	https://drive.google.com/file/d/1wqoVUMP0dDsM4msSrgolv4At7sVDkoN_/view
17	EWSR1	Present	Sequencing	EWSR1;ERG		SO:0001565#Gene Fusion					Somatic				https://drive.google.com/file/d/1tbP8mVvMa8WSbMc9nfthf3BZ5-_CEIPz/view
18	TP53	Present	Sequencing	TP53	p.R196*	SO:0001587#stop gain	SO:0002054#LOF;SO:0001786#LOH	NM_000546:c.586C>T	61.40%		Somatic				https://drive.google.com/file/d/1tKeoK2DAt3JmLjdcqJfZrd1BvQkROGl1/view
19	AR	Present	Sequencing	AR		SO:0001911#Copy number increase					Somatic				https://drive.google.com/file/d/1tKeoK2DAt3JmLjdcqJfZrd1BvQkROGl1/view
20	STK11	Present	Sequencing	STK11		SO:0002084#Exonic splice region variant	SO:0002054#LOF	NM_000455:c.465-1G>T	38.00%		Somatic				https://drive.google.com/file/d/16n9SfVqxvMvQORM_Hz5V7nDt8h2r3vMy/view
21	strata1	Present	Sequencing	TP53	p.M237I			NM_000546.5:c.711G>A	41%		Somatic				https://drive.google.com/file/d/1iFQAFDQ4f182GfyPWCm7mHELiERsfNek/view
22	strata2	Present	Sequencing	ERBB2		SO:0001880#feature_amplification					Somatic	1.9			https://drive.google.com/file/d/1iFQAFDQ4f182GfyPWCm7mHELiERsfNek/view
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