Name: rs1678971
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.

rs1678971

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:122027708 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.330893 (87584/264690, TOPMED)
A=0.326832 (45593/139500, GnomAD)
A=0.33413 (6311/18888, ALFA) (+ 12 more)
A=0.49654 (8322/16760, 8.3KJPN)
A=0.3573 (2288/6404, 1000G_30x)
A=0.3668 (1837/5008, 1000G)
A=0.3794 (1699/4478, Estonian)
A=0.4782 (1401/2930, KOREAN)
A=0.4820 (883/1832, Korea1K)
A=0.114 (114/998, GoNL)
A=0.380 (228/600, NorthernSweden)
G=0.314 (113/360, SGDP_PRJ)
A=0.407 (88/216, Qatari)
G=0.50 (6/12, Siberian)
A=0.50 (6/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BCL7A : 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	18888	G=0.66587	A=0.33413
European	Sub	14284	G=0.65815	A=0.34185
African	Sub	2946	G=0.7332	A=0.2668
African Others	Sub	114	G=0.754	A=0.246
African American	Sub	2832	G=0.7323	A=0.2677
Asian	Sub	112	G=0.589	A=0.411
East Asian	Sub	86	G=0.55	A=0.45
Other Asian	Sub	26	G=0.73	A=0.27
Latin American 1	Sub	146	G=0.671	A=0.329
Latin American 2	Sub	610	G=0.554	A=0.446
South Asian	Sub	98	G=0.55	A=0.45
Other	Sub	692	G=0.665	A=0.335

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	G=0.669107	A=0.330893
gnomAD - Genomes	Global	Study-wide	139500	G=0.673168	A=0.326832
gnomAD - Genomes	European	Sub	75634	G=0.66337	A=0.33663
gnomAD - Genomes	African	Sub	41762	G=0.72576	A=0.27424
gnomAD - Genomes	American	Sub	13570	G=0.61739	A=0.38261
gnomAD - Genomes	Ashkenazi Jewish	Sub	3308	G=0.6212	A=0.3788
gnomAD - Genomes	East Asian	Sub	3094	G=0.5048	A=0.4952
gnomAD - Genomes	Other	Sub	2132	G=0.6707	A=0.3293
Allele Frequency Aggregator	Total	Global	18888	G=0.66587	A=0.33413
Allele Frequency Aggregator	European	Sub	14284	G=0.65815	A=0.34185
Allele Frequency Aggregator	African	Sub	2946	G=0.7332	A=0.2668
Allele Frequency Aggregator	Other	Sub	692	G=0.665	A=0.335
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.554	A=0.446
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.671	A=0.329
Allele Frequency Aggregator	Asian	Sub	112	G=0.589	A=0.411
Allele Frequency Aggregator	South Asian	Sub	98	G=0.55	A=0.45
8.3KJPN	JAPANESE	Study-wide	16760	G=0.50346	A=0.49654
1000Genomes_30x	Global	Study-wide	6404	G=0.6427	A=0.3573
1000Genomes_30x	African	Sub	1786	G=0.7396	A=0.2604
1000Genomes_30x	Europe	Sub	1266	G=0.6722	A=0.3278
1000Genomes_30x	South Asian	Sub	1202	G=0.6381	A=0.3619
1000Genomes_30x	East Asian	Sub	1170	G=0.5068	A=0.4932
1000Genomes_30x	American	Sub	980	G=0.596	A=0.404
1000Genomes	Global	Study-wide	5008	G=0.6332	A=0.3668
1000Genomes	African	Sub	1322	G=0.7315	A=0.2685
1000Genomes	East Asian	Sub	1008	G=0.5050	A=0.4950
1000Genomes	Europe	Sub	1006	G=0.6610	A=0.3390
1000Genomes	South Asian	Sub	978	G=0.632	A=0.368
1000Genomes	American	Sub	694	G=0.594	A=0.406
Genetic variation in the Estonian population	Estonian	Study-wide	4478	G=0.6206	A=0.3794
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.5218	A=0.4782
Korean Genome Project	KOREAN	Study-wide	1832	G=0.5180	A=0.4820
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.886	A=0.114
Northern Sweden	ACPOP	Study-wide	600	G=0.620	A=0.380
SGDP_PRJ	Global	Study-wide	360	G=0.314	A=0.686
Qatari	Global	Study-wide	216	G=0.593	A=0.407
Siberian	Global	Study-wide	12	G=0.50	A=0.50

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 12	NC_000012.12:g.122027708G>A
GRCh38.p14 chr 12	NC_000012.12:g.122027708G>C
GRCh37.p13 chr 12	NC_000012.11:g.122465614G>A
GRCh37.p13 chr 12	NC_000012.11:g.122465614G>C

Gene: BCL7A, BAF chromatin remodeling complex subunit BCL7A (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BCL7A transcript variant 2	NM_001024808.3:c.93-2992G… NM_001024808.3:c.93-2992G>A	N/A	Intron Variant
BCL7A transcript variant 1	NM_020993.5:c.93-2992G>A	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	G=	A	C
GRCh38.p14 chr 12	NC_000012.12:g.122027708=	NC_000012.12:g.122027708G>A	NC_000012.12:g.122027708G>C
GRCh37.p13 chr 12	NC_000012.11:g.122465614=	NC_000012.11:g.122465614G>A	NC_000012.11:g.122465614G>C
BCL7A transcript variant 2	NM_001024808.1:c.93-2992=	NM_001024808.1:c.93-2992G>A	NM_001024808.1:c.93-2992G>C
BCL7A transcript variant 2	NM_001024808.3:c.93-2992=	NM_001024808.3:c.93-2992G>A	NM_001024808.3:c.93-2992G>C
BCL7A transcript variant 1	NM_020993.3:c.93-2992=	NM_020993.3:c.93-2992G>A	NM_020993.3:c.93-2992G>C
BCL7A transcript variant 1	NM_020993.5:c.93-2992=	NM_020993.5:c.93-2992G>A	NM_020993.5:c.93-2992G>C

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#.

43 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2723836	Jan 22, 2001 (92)
2	HGSV	ss77620485	Dec 07, 2007 (129)
3	HGSV	ss83511306	Dec 14, 2007 (130)
4	GMI	ss281576867	May 04, 2012 (137)
5	PJP	ss291355343	May 09, 2011 (134)
6	1000GENOMES	ss337667791	May 09, 2011 (134)
7	SSMP	ss659039772	Apr 25, 2013 (138)
8	EVA-GONL	ss990040339	Aug 21, 2014 (142)
9	1000GENOMES	ss1346950821	Aug 21, 2014 (142)
10	DDI	ss1427077228	Apr 01, 2015 (144)
11	WEILL_CORNELL_DGM	ss1933395238	Feb 12, 2016 (147)
12	GENOMED	ss1967697630	Jul 19, 2016 (147)
13	JJLAB	ss2027453657	Sep 14, 2016 (149)
14	USC_VALOUEV	ss2155809462	Dec 20, 2016 (150)
15	HUMAN_LONGEVITY	ss2193842516	Dec 20, 2016 (150)
16	GRF	ss2700169707	Nov 08, 2017 (151)
17	GNOMAD	ss2916069991	Nov 08, 2017 (151)
18	SWEGEN	ss3010478568	Nov 08, 2017 (151)
19	CSHL	ss3350285756	Nov 08, 2017 (151)
20	EGCUT_WGS	ss3677779027	Jul 13, 2019 (153)
21	EVA_DECODE	ss3694628239	Jul 13, 2019 (153)
22	ACPOP	ss3739451588	Jul 13, 2019 (153)
23	EVA	ss3751062283	Jul 13, 2019 (153)
24	KHV_HUMAN_GENOMES	ss3816390335	Jul 13, 2019 (153)
25	EVA	ss3833367121	Apr 27, 2020 (154)
26	SGDP_PRJ	ss3879276351	Apr 27, 2020 (154)
27	KRGDB	ss3928049508	Apr 27, 2020 (154)
28	KOGIC	ss3972903517	Apr 27, 2020 (154)
29	TOPMED	ss4935452563	Apr 26, 2021 (155)
30	TOMMO_GENOMICS	ss5208536106	Apr 26, 2021 (155)
31	1000G_HIGH_COVERAGE	ss5292514029	Oct 16, 2022 (156)
32	EVA	ss5408733876	Oct 16, 2022 (156)
33	HUGCELL_USP	ss5487089819	Oct 16, 2022 (156)
34	EVA	ss5510867284	Oct 16, 2022 (156)
35	1000G_HIGH_COVERAGE	ss5590868660	Oct 16, 2022 (156)
36	SANFORD_IMAGENETICS	ss5654110399	Oct 16, 2022 (156)
37	TOMMO_GENOMICS	ss5758974415	Oct 16, 2022 (156)
38	TOMMO_GENOMICS	ss5758974416	Oct 16, 2022 (156)
39	YY_MCH	ss5813714689	Oct 16, 2022 (156)
40	EVA	ss5838622406	Oct 16, 2022 (156)
41	EVA	ss5906339864	Oct 16, 2022 (156)
42	EVA	ss5945524859	Oct 16, 2022 (156)
43	EVA	ss5980766800	Oct 16, 2022 (156)
44	1000Genomes	NC_000012.11 - 122465614	Oct 12, 2018 (152)
45	1000Genomes_30x	NC_000012.12 - 122027708	Oct 16, 2022 (156)
46	Genetic variation in the Estonian population	NC_000012.11 - 122465614	Oct 12, 2018 (152)
47	gnomAD - Genomes	NC_000012.12 - 122027708	Apr 26, 2021 (155)
48	Genome of the Netherlands Release 5	NC_000012.11 - 122465614	Apr 27, 2020 (154)
49	KOREAN population from KRGDB	NC_000012.11 - 122465614	Apr 27, 2020 (154)
50	Korean Genome Project	NC_000012.12 - 122027708	Apr 27, 2020 (154)
51	Northern Sweden	NC_000012.11 - 122465614	Jul 13, 2019 (153)
52	Qatari	NC_000012.11 - 122465614	Apr 27, 2020 (154)
53	SGDP_PRJ	NC_000012.11 - 122465614	Apr 27, 2020 (154)
54	Siberian	NC_000012.11 - 122465614	Apr 27, 2020 (154)
55	8.3KJPN	NC_000012.11 - 122465614	Apr 26, 2021 (155)
56	14KJPN Submission ignored due to conflicting rows: Row 92811519 (NC_000012.12:122027707:G:A 14006/28258) Row 92811520 (NC_000012.12:122027707:G:C 1/28258)	-	Oct 16, 2022 (156)
57	14KJPN Submission ignored due to conflicting rows: Row 92811519 (NC_000012.12:122027707:G:A 14006/28258) Row 92811520 (NC_000012.12:122027707:G:C 1/28258)	-	Oct 16, 2022 (156)
58	TopMed	NC_000012.12 - 122027708	Apr 26, 2021 (155)
59	ALFA	NC_000012.12 - 122027708	Apr 26, 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).

Associated ID	History Updated (Build)
rs57960026	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77620485, ss83511306	NC_000012.9:120928333:G:A	NC_000012.12:122027707:G:A	(self)
ss281576867, ss291355343	NC_000012.10:120949996:G:A	NC_000012.12:122027707:G:A	(self)
59773395, 23517275, 14805955, 35226902, 12736453, 15437168, 31293331, 8325816, 66505413, ss337667791, ss659039772, ss990040339, ss1346950821, ss1427077228, ss1933395238, ss1967697630, ss2027453657, ss2155809462, ss2700169707, ss2916069991, ss3010478568, ss3350285756, ss3677779027, ss3739451588, ss3751062283, ss3833367121, ss3879276351, ss3928049508, ss5208536106, ss5408733876, ss5510867284, ss5654110399, ss5838622406, ss5945524859, ss5980766800	NC_000012.11:122465613:G:A	NC_000012.12:122027707:G:A	(self)
78394595, 421621671, 29281518, 150998220, 10097394123, ss2193842516, ss3694628239, ss3816390335, ss3972903517, ss4935452563, ss5292514029, ss5487089819, ss5590868660, ss5758974415, ss5813714689, ss5906339864	NC_000012.12:122027707:G:A	NC_000012.12:122027707:G:A	(self)
ss2723836	NT_009775.17:13042143:G:A	NC_000012.12:122027707:G:A	(self)
ss5758974416	NC_000012.12:122027707:G:C	NC_000012.12:122027707:G:C

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

No publications for rs1678971

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
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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

rs1678971