nstd133 - Redin et al 2016 - dbVar Study

nstd133 (Redin et al. 2016)

Organism:: Human
Study Type:: Case-Set
Submitter:: Claire Redin
Description:: Detailed breakpoint mapping of 248 balanced chromosomal rearrangements at nucleotide resolution using sequencing in subjects with congenital anomalies, based on initially provided karyotpes. See Variant Summary counts for nstd133 in dbVar Variant Summary.
Curatorial Comment:: PLEASE NOTE: All clinical variants in dbVar (including the variants in this study) have been re-accessioned in the study Clinical Structural Variants (nstd102). The new accessions are preferred and will be kept up to date with changes made in ClinVar. We recommend using the new nstd102 accessions whenever possible. A file mapping old accessions to new is available at https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/release_notes/nstd102_accession_mapping.txt.
Publication(s):: Redin et al. 2016
Last updated:: 2016-09-15

Links

Source: NCBI

Detailed Information: Download 246 Variant Regions, Download 921 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	38	93	Remapped	NC_000001.11
NC_000002.12	Chr2	49	154	Remapped	NC_000002.12
NC_000003.12	Chr3	27	62	Remapped	NC_000003.12
NC_000004.12	Chr4	18	55	Remapped	NC_000004.12
NC_000005.10	Chr5	36	126	Remapped	NC_000005.10
NC_000006.12	Chr6	32	164	Remapped	NC_000006.12
NC_000007.14	Chr7	31	92	Remapped	NC_000007.14
NC_000008.11	Chr8	14	43	Remapped	NC_000008.11
NC_000009.12	Chr9	21	87	Remapped	NC_000009.12
NC_000010.11	Chr10	20	60	Remapped	NC_000010.11
NC_000011.10	Chr11	18	47	Remapped	NC_000011.10
NC_000012.12	Chr12	17	41	Remapped	NC_000012.12
NC_000013.11	Chr13	14	32	Remapped	NC_000013.11
NC_000014.9	Chr14	28	76	Remapped	NC_000014.9
NC_000015.10	Chr15	10	23	Remapped	NC_000015.10
NC_000016.10	Chr16	12	29	Remapped	NC_000016.10
NC_000017.11	Chr17	15	37	Remapped	NC_000017.11
NC_000018.10	Chr18	13	53	Remapped	NC_000018.10
NC_000019.10	Chr19	9	19	Remapped	NC_000019.10
NC_000020.11	Chr20	9	28	Remapped	NC_000020.11
NC_000021.9	Chr21	5	12	Remapped	NC_000021.9
NC_000022.11	Chr22	6	13	Remapped	NC_000022.11
NC_000023.11	ChrX	26	67	Remapped	NC_000023.11
NC_000024.10	ChrY	2	4	Remapped	NC_000024.10
NW_017363813.1	Chr3\|NW_017363813.1	1	2	Remapped	NW_017363813.1
NW_019805488.1	Chr3\|NW_019805488.1	1	2	Remapped	NW_019805488.1
NT_187544.1	Chr4\|NT_187544.1	1	1	Remapped	NT_187544.1
NW_003315914.1	Chr4\|NW_003315914.1	1	2	Remapped	NW_003315914.1
NW_013171801.1	Chr4\|NW_013171801.1	1	2	Remapped	NW_013171801.1
NT_187548.1	Chr5\|NT_187548.1	1	2	Remapped	NT_187548.1
NT_187651.1	Chr5\|NT_187651.1	1	2	Remapped	NT_187651.1
NT_187556.1	Chr6\|NT_187556.1	3	6	Remapped	NT_187556.1
NW_003315921.1	Chr6\|NW_003315921.1	1	2	Remapped	NW_003315921.1
NW_012132918.1	Chr6\|NW_012132918.1	1	2	Remapped	NW_012132918.1
NT_187563.1	Chr7\|NT_187563.1	1	2	Remapped	NT_187563.1
NW_009646202.1	Chr10\|NW_009646202.1	1	2	Remapped	NW_009646202.1
NT_187586.1	Chr11\|NT_187586.1	1	2	Remapped	NT_187586.1
NW_018654718.1	Chr12\|NW_018654718.1	1	2	Remapped	NW_018654718.1
NT_187614.1	Chr17\|NT_187614.1	1	1	Remapped	NT_187614.1
NT_187615.1	Chr17\|NT_187615.1	1	2	Remapped	NT_187615.1
NW_003315954.1	Chr17\|NW_003315954.1	1	2	Remapped	NW_003315954.1
NW_017363819.1	Chr17\|NW_017363819.1	1	2	Remapped	NW_017363819.1
NW_014040928.1	Chr18\|NW_014040928.1	1	2	Remapped	NW_014040928.1
NW_014040929.1	Chr19\|NW_014040929.1	1	2	Remapped	NW_014040929.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	38	93	Submitted	NC_000001.10
NC_000002.11	Chr2	49	154	Submitted	NC_000002.11
NC_000003.11	Chr3	27	62	Submitted	NC_000003.11
NC_000004.11	Chr4	18	55	Submitted	NC_000004.11
NC_000005.9	Chr5	36	126	Submitted	NC_000005.9
NC_000006.11	Chr6	32	164	Submitted	NC_000006.11
NC_000007.13	Chr7	31	92	Submitted	NC_000007.13
NC_000008.10	Chr8	14	43	Submitted	NC_000008.10
NC_000009.11	Chr9	21	87	Submitted	NC_000009.11
NC_000010.10	Chr10	20	60	Submitted	NC_000010.10
NC_000011.9	Chr11	18	47	Submitted	NC_000011.9
NC_000012.11	Chr12	17	41	Submitted	NC_000012.11
NC_000013.10	Chr13	14	32	Submitted	NC_000013.10
NC_000014.8	Chr14	28	76	Submitted	NC_000014.8
NC_000015.9	Chr15	10	23	Submitted	NC_000015.9
NC_000016.9	Chr16	12	29	Submitted	NC_000016.9
NC_000017.10	Chr17	15	37	Submitted	NC_000017.10
NC_000018.9	Chr18	13	53	Submitted	NC_000018.9
NC_000019.9	Chr19	9	19	Submitted	NC_000019.9
NC_000020.10	Chr20	9	28	Submitted	NC_000020.10
NC_000021.8	Chr21	5	12	Submitted	NC_000021.8
NC_000022.10	Chr22	6	13	Submitted	NC_000022.10
NC_000023.10	ChrX	26	67	Submitted	NC_000023.10
NC_000024.9	ChrY	2	4	Submitted	NC_000024.9

Remapping summary:

			Variant Region remap status						Variant Call remap status
Sequence ID	Chr	Variant Regions on source	Perfect	Good	Pass	Fail	Mult	Variant Calls on source	Perfect	Good	Pass	Fail	Mult
NC_000001.10	Chr1	38	0	0	0	0	228	93	0	0	0	0	228
NC_000002.11	Chr2	49	0	0	0	0	394	154	0	0	0	0	394
NC_000003.11	Chr3	27	0	0	0	0	136	62	0	0	0	0	136
NC_000004.11	Chr4	18	0	0	0	0	132	55	0	0	0	0	132
NC_000005.9	Chr5	36	0	0	0	0	344	126	0	0	0	0	344
NC_000006.11	Chr6	32	0	0	0	0	516	164	0	0	0	0	516
NC_000007.13	Chr7	31	0	0	0	0	242	92	0	0	0	0	242
NC_000008.10	Chr8	14	0	0	0	0	104	43	0	0	0	0	104
NC_000009.11	Chr9	21	0	0	0	0	264	87	0	0	0	0	264
NC_000010.10	Chr10	20	0	0	0	0	156	60	0	0	0	0	156
NC_000011.9	Chr11	18	0	0	0	0	112	47	0	0	0	0	112
NC_000012.11	Chr12	17	0	0	0	0	104	41	0	0	0	0	104
NC_000013.10	Chr13	14	0	0	0	0	72	32	0	0	0	0	72
NC_000014.8	Chr14	28	0	0	0	0	184	76	0	0	0	0	184
NC_000015.9	Chr15	10	0	0	0	0	52	23	0	0	0	0	52
NC_000016.9	Chr16	12	0	0	0	0	60	29	0	0	0	0	60
NC_000017.10	Chr17	15	0	0	0	0	86	37	0	0	0	0	86
NC_000018.9	Chr18	13	0	0	0	0	138	53	0	0	0	0	138
NC_000019.9	Chr19	9	0	0	0	0	40	19	0	0	0	0	40
NC_000020.10	Chr20	9	0	0	0	0	64	28	0	0	0	0	64
NC_000021.8	Chr21	5	0	0	0	0	24	12	0	0	0	0	24
NC_000022.10	Chr22	6	0	0	0	0	28	13	0	0	0	0	28
NC_000023.10	ChrX	26	0	0	0	0	196	67	0	0	0	0	196
NC_000024.9	ChrY	2	0	0	0	0	8	4	0	0	0	0	8

Samplesets

Number of Samplesets: 1

Name:: Mapped_BCAs
Description:: 248 sucessfully mapped rearrangements
Size:: 248
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Abnormality of prenatal development or birth
Neurodevelopmental abnormality
Phenotypic abnormality

Samples for sampleset 1 (displaying 100 of the 248 samples)
Sample ID	Subject ID	Sex	Subject Phenotype
DGAP054	DGAP054	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP191	DGAP191	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP143	DGAP143	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP137	DGAP137	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP031	DGAP031	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP182	DGAP182	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP189	DGAP189	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP142	DGAP142	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP138	DGAP138	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP218	DGAP218	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP162	DGAP162	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP055	DGAP055	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP171	DGAP171	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP219	DGAP219	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP134	DGAP134	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP108	DGAP108	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP145	DGAP145	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP125	DGAP125	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP203	DGAP203	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP180	DGAP180	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP168	DGAP168	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP230	DGAP230	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP195	DGAP195	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP155	DGAP155	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP163	DGAP163	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP113	DGAP113	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP032	DGAP032	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP154	DGAP154	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP124	DGAP124	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP174	DGAP174	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP139	DGAP139	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP187	DGAP187	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP152	DGAP152	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP091	DGAP091	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP018	DGAP018	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP186	DGAP186	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP169	DGAP169	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP099	DGAP099	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP101	DGAP101	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP224	DGAP224	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP197	DGAP197	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP161	DGAP161	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP147	DGAP147	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP190	DGAP190	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP001	DGAP001	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP107	DGAP107	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP112	DGAP112	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP192	DGAP192	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP167	DGAP167	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP159	DGAP159	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP151	DGAP151	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP170	DGAP170	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP003	DGAP003	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP199	DGAP199	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP120	DGAP120	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP232	DGAP232	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP002	DGAP002	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP132	DGAP132	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP012	DGAP012	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP235	DGAP235	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP017	DGAP017	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP121	DGAP121	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP172	DGAP172	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP173	DGAP173	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP105	DGAP105	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP093	DGAP093	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP200	DGAP200	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP069	DGAP069	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP198	DGAP198	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP097	DGAP097	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP153	DGAP153	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP166	DGAP166	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP126	DGAP126	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP183	DGAP183	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP179	DGAP179	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP202	DGAP202	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP237	DGAP237	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP111	DGAP111	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP196	DGAP196	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP157	DGAP157	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP220	DGAP220	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP127	DGAP127	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP096	DGAP096	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP131	DGAP131	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP193	DGAP193	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP100	DGAP100	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP164	DGAP164	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP233	DGAP233	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP122	DGAP122	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP201	DGAP201	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP222	DGAP222	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP130	DGAP130	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP223	DGAP223	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP176	DGAP176	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP090	DGAP090	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP211	DGAP211	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP011	DGAP011	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP133	DGAP133	Male	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP148	DGAP148	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality
DGAP225	DGAP225	Female	abnormality of prenatal development or birth neurodevelopmental abnormality phenotypic abnormality

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	Sequencing	Split read and paired-end mapping	755
2	Discovery	Sequencing	Split read mapping	83
3	Discovery	Sequencing	Split read and paired-end mapping	66
4	Discovery	Merging of experiments 1,2	Merging of experiments 1,2	17

dbVar

Database of genomic structural variation

nstd133 (Redin et al. 2016)

Links

Detailed Information: Download 246 Variant Regions, Download 921 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd133 (Redin et al. 2016)

Links

Detailed Information: Download 246 Variant Regions, Download 921 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37 (hg19)

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: