Name: rs200178061
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs200178061

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:147572221-147572222 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: delA
Variation Type: Indel Insertion and Deletion
Frequency: delA=0.017103 (4527/264690, TOPMED)
delA=0.014500 (2033/140206, GnomAD)
delA=0.04290 (1212/28254, 14KJPN) (+ 12 more)
delA=0.01199 (222/18520, ALFA)
delA=0.04385 (735/16760, 8.3KJPN)
delA=0.0255 (163/6404, 1000G_30x)
delA=0.0256 (128/5008, 1000G)
delA=0.0112 (50/4480, Estonian)
delA=0.0150 (58/3854, ALSPAC)
delA=0.0119 (44/3708, TWINSUK)
delA=0.0622 (114/1832, Korea1K)
delA=0.011 (11/998, GoNL)
delA=0.007 (4/600, NorthernSweden)
delA=0.048 (10/210, Vietnamese)
delA=0.03 (1/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BCL9 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18520	AA=0.98801	A=0.01199
European	Sub	14152	AA=0.98876	A=0.01124
African	Sub	2898	AA=0.9872	A=0.0128
African Others	Sub	114	AA=0.991	A=0.009
African American	Sub	2784	AA=0.9871	A=0.0129
Asian	Sub	112	AA=0.929	A=0.071
East Asian	Sub	86	AA=0.91	A=0.09
Other Asian	Sub	26	AA=1.00	A=0.00
Latin American 1	Sub	146	AA=0.986	A=0.014
Latin American 2	Sub	610	AA=0.993	A=0.007
South Asian	Sub	98	AA=0.98	A=0.02
Other	Sub	504	AA=0.980	A=0.020

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	AA=0.982897	delA=0.017103
gnomAD - Genomes	Global	Study-wide	140206	AA=0.985500	delA=0.014500
gnomAD - Genomes	European	Sub	75940	AA=0.98870	delA=0.01130
gnomAD - Genomes	African	Sub	42020	AA=0.98315	delA=0.01685
gnomAD - Genomes	American	Sub	13642	AA=0.98534	delA=0.01466
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	AA=0.9846	delA=0.0154
gnomAD - Genomes	East Asian	Sub	3132	AA=0.9428	delA=0.0572
gnomAD - Genomes	Other	Sub	2150	AA=0.9828	delA=0.0172
14KJPN	JAPANESE	Study-wide	28254	AA=0.95710	delA=0.04290
Allele Frequency Aggregator	Total	Global	18520	AA=0.98801	delA=0.01199
Allele Frequency Aggregator	European	Sub	14152	AA=0.98876	delA=0.01124
Allele Frequency Aggregator	African	Sub	2898	AA=0.9872	delA=0.0128
Allele Frequency Aggregator	Latin American 2	Sub	610	AA=0.993	delA=0.007
Allele Frequency Aggregator	Other	Sub	504	AA=0.980	delA=0.020
Allele Frequency Aggregator	Latin American 1	Sub	146	AA=0.986	delA=0.014
Allele Frequency Aggregator	Asian	Sub	112	AA=0.929	delA=0.071
Allele Frequency Aggregator	South Asian	Sub	98	AA=0.98	delA=0.02
8.3KJPN	JAPANESE	Study-wide	16760	AA=0.95615	delA=0.04385
1000Genomes_30x	Global	Study-wide	6404	AA=0.9745	delA=0.0255
1000Genomes_30x	African	Sub	1786	AA=0.9849	delA=0.0151
1000Genomes_30x	Europe	Sub	1266	AA=0.9905	delA=0.0095
1000Genomes_30x	South Asian	Sub	1202	AA=0.9692	delA=0.0308
1000Genomes_30x	East Asian	Sub	1170	AA=0.9410	delA=0.0590
1000Genomes_30x	American	Sub	980	AA=0.982	delA=0.018
1000Genomes	Global	Study-wide	5008	AA=0.9744	delA=0.0256
1000Genomes	African	Sub	1322	AA=0.9856	delA=0.0144
1000Genomes	East Asian	Sub	1008	AA=0.9405	delA=0.0595
1000Genomes	Europe	Sub	1006	AA=0.9920	delA=0.0080
1000Genomes	South Asian	Sub	978	AA=0.970	delA=0.030
1000Genomes	American	Sub	694	AA=0.983	delA=0.017
Genetic variation in the Estonian population	Estonian	Study-wide	4480	AA=0.9888	delA=0.0112
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	AA=0.9850	delA=0.0150
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	AA=0.9881	delA=0.0119
Korean Genome Project	KOREAN	Study-wide	1832	AA=0.9378	delA=0.0622
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	AA=0.989	delA=0.011
Northern Sweden	ACPOP	Study-wide	600	AA=0.993	delA=0.007
A Vietnamese Genetic Variation Database	Global	Study-wide	210	AA=0.952	delA=0.048
The Danish reference pan genome	Danish	Study-wide	40	AA=0.97	delA=0.03

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 1	NC_000001.11:g.147572222del
GRCh37.p13 chr 1 fix patch HG1287_PATCH	NW_003871055.3:g.4387635del
GRCh37.p13 chr 1	NC_000001.10:g.147044013del

Gene: BCL9, BCL9 transcription coactivator (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BCL9 transcript	NM_004326.4:c.-478+30548d… NM_004326.4:c.-478+30548del	N/A	Intron Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	AA=	delA
GRCh38.p14 chr 1	NC_000001.11:g.147572221_147572222=	NC_000001.11:g.147572222del
GRCh37.p13 chr 1 fix patch HG1287_PATCH	NW_003871055.3:g.4387634_4387635=	NW_003871055.3:g.4387635del
GRCh37.p13 chr 1	NC_000001.10:g.147044012_147044013=	NC_000001.10:g.147044013del
BCL9 transcript	NM_004326.3:c.-478+30568=	NM_004326.3:c.-478+30569del
BCL9 transcript	NM_004326.4:c.-478+30547=	NM_004326.4:c.-478+30548del
BCL9 transcript variant X2	XM_005272972.1:c.-478+30568=	XM_005272972.1:c.-478+30569del
BCL9 transcript variant X3	XM_005272973.1:c.-478+30568=	XM_005272973.1:c.-478+30569del
BCL9 transcript variant X2	XM_005277417.1:c.-478+30547=	XM_005277417.1:c.-478+30548del
BCL9 transcript variant X3	XM_005277418.1:c.-478+30547=	XM_005277418.1:c.-478+30548del

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

32 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss498990614	May 04, 2012 (137)
2	TISHKOFF	ss553777205	Apr 25, 2013 (138)
3	SSMP	ss663118644	Apr 09, 2015 (144)
4	EVA-GONL	ss975645435	Apr 09, 2015 (144)
5	1000GENOMES	ss1367840655	Aug 28, 2014 (142)
6	EVA_GENOME_DK	ss1574019994	Apr 09, 2015 (144)
7	EVA_DECODE	ss1585027271	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1701203194	Apr 09, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1701203305	Apr 09, 2015 (144)
10	JJLAB	ss2030347450	Sep 28, 2016 (149)
11	SYSTEMSBIOZJU	ss2624485096	Oct 11, 2018 (152)
12	GNOMAD	ss2760727212	Oct 11, 2018 (152)
13	SWEGEN	ss2987658643	Oct 11, 2018 (152)
14	MCHAISSO	ss3064423198	Nov 08, 2017 (151)
15	EGCUT_WGS	ss3655637624	Jul 12, 2019 (153)
16	EVA_DECODE	ss3687703871	Jul 12, 2019 (153)
17	ACPOP	ss3727453881	Jul 12, 2019 (153)
18	KHV_HUMAN_GENOMES	ss3799765476	Jul 12, 2019 (153)
19	EVA	ss3826406798	Apr 25, 2020 (154)
20	KOGIC	ss3945553518	Apr 25, 2020 (154)
21	GNOMAD	ss4002738004	Apr 25, 2021 (155)
22	TOPMED	ss4466776285	Apr 25, 2021 (155)
23	TOMMO_GENOMICS	ss5146225776	Apr 25, 2021 (155)
24	1000G_HIGH_COVERAGE	ss5244131832	Oct 12, 2022 (156)
25	HUGCELL_USP	ss5444772579	Oct 12, 2022 (156)
26	1000G_HIGH_COVERAGE	ss5517380633	Oct 12, 2022 (156)
27	SANFORD_IMAGENETICS	ss5626499056	Oct 12, 2022 (156)
28	TOMMO_GENOMICS	ss5673368911	Oct 12, 2022 (156)
29	YY_MCH	ss5801221885	Oct 12, 2022 (156)
30	EVA	ss5832605059	Oct 12, 2022 (156)
31	EVA	ss5910101155	Oct 12, 2022 (156)
32	EVA	ss5938309638	Oct 12, 2022 (156)
33	1000Genomes	NC_000001.10 - 147044012	Oct 11, 2018 (152)
34	1000Genomes_30x	NC_000001.11 - 147572221	Oct 12, 2022 (156)
35	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 147044012	Oct 11, 2018 (152)
36	Genetic variation in the Estonian population	NC_000001.10 - 147044012	Oct 11, 2018 (152)
37	The Danish reference pan genome	NC_000001.10 - 147044012	Apr 25, 2020 (154)
38	gnomAD - Genomes	NC_000001.11 - 147572221	Apr 25, 2021 (155)
39	Genome of the Netherlands Release 5	NC_000001.10 - 147044012	Apr 25, 2020 (154)
40	Korean Genome Project	NC_000001.11 - 147572221	Apr 25, 2020 (154)
41	Northern Sweden	NC_000001.10 - 147044012	Jul 12, 2019 (153)
42	8.3KJPN	NC_000001.10 - 147044012	Apr 25, 2021 (155)
43	14KJPN	NC_000001.11 - 147572221	Oct 12, 2022 (156)
44	TopMed	NC_000001.11 - 147572221	Apr 25, 2021 (155)
45	UK 10K study - Twins	NC_000001.10 - 147044012	Oct 11, 2018 (152)
46	A Vietnamese Genetic Variation Database	NC_000001.10 - 147044012	Jul 12, 2019 (153)
47	ALFA	NC_000001.11 - 147572221	Apr 25, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1585027271	NC_000001.9:145510635:A:	NC_000001.11:147572220:AA:A	(self)
3547297, 1936542, 1375872, 170855, 843503, 738746, 4195083, 1936542, 418737, ss498990614, ss663118644, ss975645435, ss1367840655, ss1574019994, ss1701203194, ss1701203305, ss2030347450, ss2624485096, ss2760727212, ss2987658643, ss3655637624, ss3727453881, ss3826406798, ss5146225776, ss5626499056, ss5832605059, ss5938309638	NC_000001.10:147044011:A:	NC_000001.11:147572220:AA:A	(self)
ss553777205	NC_000001.10:147044012:A:	NC_000001.11:147572220:AA:A	(self)
4906568, 25718264, 1931519, 7206015, 30382620, ss3064423198, ss3687703871, ss3799765476, ss3945553518, ss4002738004, ss4466776285, ss5244131832, ss5444772579, ss5517380633, ss5673368911, ss5801221885, ss5910101155	NC_000001.11:147572220:A:	NC_000001.11:147572220:AA:A	(self)
3612860436	NC_000001.11:147572220:AA:A	NC_000001.11:147572220:AA:A	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs200178061

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs200178061