Joint Open Genome and Omics Platform (JoGo)

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geneid	728036
ensemblid	ENSG00000224089.3
hgncid	33291
symbol	CT47A10
name	cancer/testis antigen family 47 member A10
refseq_nuc	NM_001080137.2
refseq_prot	NP_001073606.1
ensembl_nuc	ENST00000430448.3
ensembl_prot	ENSP00000411909.2
mane_status	MANE Select
chr	chrX
start	120938701
end	120942023
strand	-
ver	v1.2
region	chrX:120938701-120942023
region5000	chrX:120933701-120947023
regionname0	CT47A10_chrX_120938701_120942023
regionname5000	CT47A10_chrX_120933701_120947023

ahapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	alen	total	AFR	AMR	EAS	EUR	SAS	JPT	regionname	genename	aa	chr	start	end
a0001	0/0	288	6	0	0	6	0	0	5	CT47A10_chrX_120933701_120947023	CT47A10	copy fasta	chrX	120933701	120947023
a0002	0/0	31	1	0	0	1	0	0	0	CT47A10_chrX_120933701_120947023	CT47A10	copy fasta	chrX	120933701	120947023

chapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	clen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	cseq	chr	start	end
c0001	0/0	867	6	0	0	6	0	0	CT47A10_chrX_120933701_120947023	CT47A10	copy fasta	chrX	120933701	120947023
c0002	0/0	871	1	0	0	1	0	0	CT47A10_chrX_120933701_120947023	CT47A10	copy fasta	chrX	120933701	120947023

thapid	grch38 chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
t0001	0/0	432	6	0	0	6	0	0	CT47A10_chrX_120933701_120947023	CT47A10	copy fasta	chrX	120933701	120947023
t0002	0/0	431	1	0	0	1	0	0	CT47A10_chrX_120933701_120947023	CT47A10	copy fasta	chrX	120933701	120947023

ghapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	chr	start	end
g0001	0/0	2	0	0	2	0	0	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
g0002	0/0	2	0	0	2	0	0	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
g0003	0/0	1	0	0	1	0	0	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
g0004	0/0	1	0	0	1	0	0	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
g0005	0/0	1	0	0	1	0	0	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023

achapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	clen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	cseq	chr	start	end
a0001c0001	0/0	867	6	0	0	6	0	0	CT47A10_chrX_120933701_120947023	CT47A10	copy fasta	chrX	120933701	120947023
a0002c0002	0/0	871	1	0	0	1	0	0	CT47A10_chrX_120933701_120947023	CT47A10	copy fasta	chrX	120933701	120947023

acthapid	grch38 chm13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
a0001c0001t0001	0/0	1298	5	0	0	5	0	0	CT47A10_chrX_120933701_120947023	CT47A10	copy fasta	chrX	120933701	120947023
a0001c0001t0002	0/0	1297	1	0	0	1	0	0	CT47A10_chrX_120933701_120947023	CT47A10	copy fasta	chrX	120933701	120947023
a0002c0002t0001	0/0	1302	1	0	0	1	0	0	CT47A10_chrX_120933701_120947023	CT47A10	copy fasta	chrX	120933701	120947023

actghapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	chr	start	end
a0001c0001t0001g0001	0/0	2	0	0	2	0	0	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
a0001c0001t0001g0002	0/0	2	0	0	2	0	0	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
a0001c0001t0001g0003	0/0	1	0	0	1	0	0	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
a0001c0001t0002g0004	0/0	1	0	0	1	0	0	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
a0002c0002t0001g0005	0/0	1	0	0	1	0	0	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023

sampleid	ID haplotypeid	ahapid	chapid	thapid	ghapid	gpopname	popname	regionname	genename	chr	start	end
HG00597	hp1	a0002	c0002	t0001	g0005	EAS	CHS	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
HG00597	hp2	a0001	c0001	t0001	g0003	EAS	CHS	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
NA18959	hp1	a0001	c0001	t0002	g0004	EAS	JPT	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
NA18967	hp1	a0001	c0001	t0001	g0002	EAS	JPT	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
NA18995	hp1	a0001	c0001	t0001	g0001	EAS	JPT	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
NA19066	hp1	a0001	c0001	t0001	g0002	EAS	JPT	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023
NA19086	hp1	a0001	c0001	t0001	g0001	EAS	JPT	CT47A10_chrX_120933701_120947023	CT47A10	chrX	120933701	120947023

chr:pos	ref	alt	# # of ahapid:amino-acid(protein) level	ahapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos
chrX:120941044	G G	C C	1	a0002 a0002	1	HG00597.hp1 HG00597.hp1	missense_variant	MODERATE	c.721C>G c.721C>G	p.Gln241Glu p.Gln241Glu	CT47A10	ENSG00000224089.3	transcript	ENST00000430448.3	protein_coding	1/3	980/1298	721/867	241/288			chrX	120941044
chrX:120941045	T T	TG TG	1	a0002 a0002	1	HG00597.hp1 HG00597.hp1	frameshift_variant	HIGH	c.719dupC c.719dupC	p.Gln241fs p.Gln241fs	CT47A10	ENSG00000224089.3	transcript	ENST00000430448.3	protein_coding	1/3	978/1298	719/867	240/288			chrX	120941045
chrX:120941059	C C	CTG CTG	1	a0002 a0002	1	HG00597.hp1 HG00597.hp1	frameshift_variant	HIGH	c.704_705dupCA c.704_705dupCA	p.Glu236fs p.Glu236fs	CT47A10	ENSG00000224089.3	transcript	ENST00000430448.3	protein_coding	1/3	964/1298	705/867	235/288			chrX	120941059
chrX:120941699	T T	TC TC	1	a0002 a0002	1	HG00597.hp1 HG00597.hp1	frameshift_variant	HIGH	c.65dupG c.65dupG	p.Ala23fs p.Ala23fs	CT47A10	ENSG00000224089.3	transcript	ENST00000430448.3	protein_coding	1/3	324/1298	65/867	22/288			chrX	120941699

chr:pos	ref	alt	# # of chapid	chapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos

chr:pos	ref	alt	# # of thapid:transcript level	thapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos
chrX:120938731	AT AT	A A	1	a0001c0001t0002 a0001c0001t0002	1	NA18959.hp1 NA18959.hp1	3_prime_UTR_variant	MODIFIER	c.141delA c.141delA		CT47A10	ENSG00000224089.3	transcript	ENST00000430448.3	protein_coding	3/3				1279		chrX	120938731

chr:pos	ref	alt	# # of ghapid:genebody level	ghapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	genebody_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos
chrX:120938895	A A	G G	1	a0001c0001t0001g0003 a0001c0001t0001g0003	1	HG00597.hp2 HG00597.hp2	intron_variant	MODIFIER	c.32-54T>C c.32-54T>C		CT47A10	ENSG00000224089.3	transcript	ENST00000430448.3	protein_coding	2/2						chrX	120938895
chrX:120939768	G G	A A	1	a0001c0001t0001g0002 a0001c0001t0001g0002	2	NA18967.hp1 NA19066.hp1 NA18967.hp1 NA19066.hp1	intron_variant	MODIFIER	c.31+212C>T c.31+212C>T		CT47A10	ENSG00000224089.3	transcript	ENST00000430448.3	protein_coding	2/2						chrX	120939768
chrX:120940943	G G	GC GC	1	a0002c0002t0001g0005 a0002c0002t0001g0005	1	HG00597.hp1 HG00597.hp1	intron_variant	MODIFIER	c.742+79dupG c.742+79dupG		CT47A10	ENSG00000224089.3	transcript	ENST00000430448.3	protein_coding	1/2						chrX	120940943