KarReporter - test

Fully Supported Clustered SVs

SVs

1. ins-t(2;2)(q31.2;q36.1q36.1): balanced non-reciprocal translocation of Chr2: 221,204,994-221,284,178 (q36.1 - q36.1) into Chr2: 178,043,170 (q31.2)

Disrupted DDG2P Genes

None Found

Partially Supported Clustered SVs

SVs

2. ins(14;2)(q36.1;q36.1q31.2): duplicated-insertion of Chr2: 221,204,993-178,043,170 (q36.1 - q31.2) into Chr14: 221,284,178 (q36.1)

Disrupted DDG2P Genes

SV	gene	rationale	allelic req.	mutatation req.	confidence	organ
1	BRF1	breakpoint proximal	biallelic autosomal	absent gene product	definitive	Brain/Cognition
1	JAG2	breakpoint proximal	biallelic autosomal	absent gene product	strong	Musculature
1	TTN	CN+1	biallelic autosomal	absent gene product	definitive	Musculature; Heart/Cardiovasculature/Lymphatic
1	NCKAP1	CN+1	monoallelic autosomal	absent gene product	limited	Brain/Cognition
1	HIBCH	CN+1	biallelic autosomal	absent gene product	definitive	Endocrine/Metabolic; Brain/Cognition
1	HECW2	CN+1	biallelic autosomal	decreased gene product level	limited	nan
1	PGAP1	CN+1	biallelic autosomal	absent gene product	strong	Endocrine/Metabolic; Brain/Cognition
1	HSPD1	CN+1	biallelic autosomal	absent gene product	strong	Brain/Cognition
1	SATB2	CN+1	monoallelic autosomal	absent gene product	definitive	Face; Skeleton; Brain/Cognition
1	NDUFB3	CN+1	biallelic autosomal	absent gene product	definitive	nan
1	TMEM237	CN+1	biallelic autosomal	absent gene product	definitive	Brain/Cognition
1	ALS2	CN+1	biallelic autosomal	absent gene product	definitive	Spinal cord/Peripheral nerves; Brain/Cognition
1	SUMO1	CN+1	monoallelic autosomal	absent gene product	limited	Face
1	NDUFS1	CN+1	biallelic autosomal	altered gene product structure	definitive	Endocrine/Metabolic; Brain/Cognition
1	EEF1B2	CN+1	biallelic autosomal	absent gene product	limited	Brain/Cognition
1	KLF7	CN+1	monoallelic autosomal	altered gene product structure	definitive	Brain/Cognition
1	FZD5	CN+1	monoallelic autosomal	altered gene product structure	strong	Eye: Structure
1	CRYGD	CN+1	monoallelic autosomal	absent gene product	limited	Eye
1	CRYGC	CN+1	monoallelic autosomal	absent gene product	definitive	Eye
1	UNC80	CN+1	biallelic autosomal	absent gene product	definitive	Brain/Cognition
1	MYL1	CN+1	biallelic autosomal	absent gene product	limited	Spinal cord/Peripheral nerves
1	CPS1	CN+1	biallelic autosomal	absent gene product	definitive	Endocrine/Metabolic; Brain/Cognition
1	ATIC	CN+1	biallelic autosomal	absent gene product	definitive	Endocrine/Metabolic; Brain/Cognition
1	FN1	CN+1	monoallelic autosomal	altered gene product structure	strong	Skeleton
1	PECR	CN+1	biallelic autosomal	altered gene product structure	limited	Brain/Cognition
1	SMARCAL1	CN+1	biallelic autosomal	absent gene product	definitive	Bone Marrow/Immune; Skeleton; Eye; Skin; Kidney Renal Tract; Face; Endocrine/Metabolic; Brain/Cognition; Hair/Nails; Teeth and Dentition
1	ZNF142	CN+1	biallelic autosomal	absent gene product	strong	Brain/Cognition
1	BCS1L	CN+1	biallelic autosomal	absent gene product	definitive	Skeleton; Endocrine/Metabolic; GI tract
1	CYP27A1	CN+1	biallelic autosomal	absent gene product	definitive	Skeleton; Spinal cord/Peripheral nerves; Eye; Skin; Endocrine/Metabolic; Brain/Cognition; Eye: Lens; Heart/Cardiovasculature/Lymphatic
1	IHH	CN+1	biallelic autosomal	altered gene product structure	definitive	Skeleton
1	ABCB6	CN+1	monoallelic autosomal	altered gene product structure	limited	Eye: Structure; Eye
1	SPEG	CN+1	biallelic autosomal	absent gene product	definitive	Musculature; Heart/Cardiovasculature/Lymphatic
1	GMPPA	CN+1	biallelic autosomal	absent gene product	definitive	Endocrine/Metabolic; Brain/Cognition
1	OBSL1	CN+1	biallelic autosomal	absent gene product	definitive	Skeleton; Brain/Cognition

OMKar Output

Chromosomes

2: [4+, 5+, 6+, 7+, 8+, 9+]

5: [4+, 5+, 6+, 7+, 9+]

3: [45+, 46+, 47+, 48+]

4: [45+, 46+, 47+, 8-, 7-, 48+]

Segment List

Segment	chr	start	end	size
4	Chr2	15,925	92,188,145	92,172,221
5	Chr2	92,188,146	94,090,557	1,902,412
6	Chr2	94,090,558	178,043,169	83,952,612
7	Chr2	178,043,170	221,204,993	43,161,824
8	Chr2	221,204,994	221,284,178	79,185
9	Chr2	221,284,179	242,181,356	20,897,178
45	Chr14	0	16,000,000	16,000,001
46	Chr14	16,000,001	18,173,523	2,173,523
47	Chr14	18,173,524	105,159,387	86,985,864
48	Chr14	105,159,388	106,873,282	1,713,895

SV calls not incorporated

chromosome	start	end	SV_type	smap_id	confidence
2	91434682.0	91643851.0	duplication_inverted	1793	-1.0
2	91834734.0	91834734.0	inversion	1803	0.84
2	91834734.0	91834734.0	inversion	1807	0.93
2	94196559.0	94280827.0	duplication_inverted	1815	-1.0
2	94196559.0	94280827.0	duplication_inverted	1818	-1.0
2	94196559.0	94280827.0	duplication_inverted	1821	-1.0
14	19189529.0	19620470.0	inversion	11441	0.77
14	19126837.0	19947403.0	duplication_split	11451	-1.0
14	19126837.0	19947403.0	duplication_split	11454	-1.0
14	20882922.0	20949151.0	deletion	11461	0.99

Fully Supported Clustered SVs

SVs

1. del(12)(p13.31): deletion on Chr12: 9,476,202-9,580,571 (p13.31 - p13.31)

Disrupted DDG2P Genes

None Found

Partially Supported Clustered SVs

None

OMKar Output

Chromosomes

24: [37+, 38+, 39+, 40+, 41+]

25: [37+, 39+, 40+, 41+]

Segment List

Segment	chr	start	end	size
37	Chr12	14,569	9,476,201	9,461,633
38	Chr12	9,476,202	9,580,571	104,370
39	Chr12	9,580,572	34,769,407	25,188,836
40	Chr12	34,769,408	37,185,252	2,415,845
41	Chr12	37,185,253	133,263,959	96,078,707

SV calls not incorporated

chromosome	start	end	SV_type	smap_id	confidence
12	9476201.5	9580571.0	deletion	10213	0.99
12	9476201.5	9580571.0	deletion	10256	0.99
12	11352845.0	11392565.0	duplication	10263	-1.0

Fully Supported Clustered SVs

None

Partially Supported Clustered SVs

SVs

1. dup(16)(p11.2): tandem duplication on Chr16: 32,264,687-32,964,090 (p11.2 - p11.2)

Disrupted DDG2P Genes

None Found

OMKar Output

Chromosomes

30: [52+, 53+, 54+, 55+, 56+]

31: [52+, 53+, 53+, 54+, 55+, 56+]

Segment List

Segment	chr	start	end	size
52	Chr16	14,135	32,264,686	32,250,552
53	Chr16	32,264,687	32,964,090	699,404
54	Chr16	32,964,091	36,311,158	3,347,068
55	Chr16	36,311,159	38,280,682	1,969,524
56	Chr16	38,280,683	90,224,750	51,944,068

SV calls not incorporated

chromosome	start	end	SV_type	smap_id	confidence
16	14905245.0	15322465.0	inversion	12450	0.8
16	14819366.0	14905245.0	duplication_inverted	12453	-1.0
16	21394702.0	21557960.0	duplication	12501	-1.0
16	21557960.0	22543925.5	inversion	12502	1.0
16	21394702.0	21557960.0	duplication	12511	-1.0
16	21557960.0	22543925.5	inversion	12512	1.0
16	22543925.5	22690602.0	duplication_inverted	12533	-1.0
16	29498408.0	30318984.5	deletion	12534	0.99
16	22543925.5	22690602.0	duplication_inverted	12567	-1.0
16	28645339.0	28645339.0	inversion	12571	0.72
16	28645339.0	28645339.0	inversion	12574	0.7
16	32264687.0	32281637.0	duplication_inverted	12590	-1.0
16	32914040.0	33499296.0	inversion	12597	0.7
16	33499296.0	33625444.0	duplication	12610	-1.0
16	33499296.0	33625444.0	duplication	12611	-1.0
16	75515109.5	75538476.0	duplication	12767	-1.0

Fully Supported Clustered SVs

SVs

1. del(17)(q21.31): deletion on Chr17: 46,284,336-46,702,870 (q21.31 - q21.31)

Disrupted DDG2P Genes

None Found

Partially Supported Clustered SVs

None

OMKar Output

Chromosomes

32: [57+, 58+, 59+, 60+, 61+]

33: [57+, 58+, 59+, 61+]

Segment List

Segment	chr	start	end	size
57	Chr17	66,654	22,813,679	22,747,026
58	Chr17	22,813,680	26,885,980	4,072,301
59	Chr17	26,885,981	46,284,335	19,398,355
60	Chr17	46,284,336	46,702,870	418,535
61	Chr17	46,702,871	83,246,391	36,543,521

SV calls not incorporated

chromosome	start	end	SV_type	smap_id	confidence
17	36110318.0	36244236.0	duplication_inverted	13021	-1.0
17	36180738.0	36443527.0	duplication	13042	-1.0
17	36228425.0	36228425.0	inversion	13043	0.98
17	38150377.0	38176102.0	duplication_inverted	13052	-1.0
17	36287607.0	36392615.0	duplication_inverted	13055	-1.0
17	37920275.0	38046570.0	inversion	13056	0.99
17	37920275.0	38046570.0	deletion	13058	0.99
17	38179195.0	38196128.0	inversion	13063	1.0
17	38196128.0	38243087.0	duplication_inverted	13101	-1.0
17	45552764.0	45587109.0	duplication_inverted	13114	-1.0
17	45552764.0	45587109.0	duplication_inverted	13125	-1.0
17	59815554.0	60023682.0	duplication_inverted	13187	-1.0
17	59784560.0	60023682.0	duplication_inverted	13189	-1.0
17	60122859.0	60323946.0	duplication_inverted	13200	-1.0
17	60122859.0	60323946.0	duplication_inverted	13201	-1.0

Fully Supported Clustered SVs

None

Partially Supported Clustered SVs

SVs

1. del(22)(q11.21): deletion on Chr22: 18,181,893-21,167,062 (q11.21 - q11.21)
2. ins(22)(q11.1q11.21q11.21): duplicated-insertion of Chr22: 21,167,062-18,921,117 (q11.21 - q11.21) into Chr22: 15,054,319 (q11.1)

Disrupted DDG2P Genes

SV	gene	rationale	allelic req.	mutatation req.	confidence	organ
1	TUBA8	breakpoint proximal	biallelic autosomal	absent gene product	limited	Brain/Cognition; Eye
1	USP18	breakpoint proximal	biallelic autosomal	absent gene product	strong	Lungs; Skeleton; Multisystem; Brain/Cognition
1	TUBA8	CN-1	biallelic autosomal	absent gene product	limited	Brain/Cognition; Eye
1	USP18	CN-1	biallelic autosomal	absent gene product	strong	Lungs; Skeleton; Multisystem; Brain/Cognition

OMKar Output

Chromosomes

42: [74+, 75+, 76+, 77+, 78+, 79+]

43: [74+, 75+, 76+, 78-, 79+]

Segment List

Segment	chr	start	end	size
74	Chr22	10,514,804	12,954,788	2,439,985
75	Chr22	12,954,789	15,054,318	2,099,530
76	Chr22	15,054,319	18,181,892	3,127,574
77	Chr22	18,181,893	18,921,116	739,224
78	Chr22	18,921,117	21,167,062	2,245,946
79	Chr22	21,167,063	50,805,586	29,638,524

SV calls not incorporated

chromosome	start	end	SV_type	smap_id	confidence
22	11370078.5	12279864.0	deletion	14873	0.99
22	11370078.5	12491863.0	inversion	14874	0.99
22	11370078.5	12279864.0	deletion	14876	0.99
22	11370078.5	12279864.0	deletion	14879	0.99
22	15522454.0	15875120.0	duplication	14925	-1.0
22	18181891.5	18876658.0	inversion	14942	1.0
22	18181891.5	18876658.0	deletion	14944	0.99
22	21145833.0	21188290.5	inversion	14963	1.0
22	21188290.5	21188290.5	inversion	14976	1.0