Name: rs142704172
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.

rs142704172

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:122058988 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.005421 (1435/264690, TOPMED)
T=0.006189 (868/140248, GnomAD)
T=0.00900 (170/18890, ALFA) (+ 12 more)
T=0.0105 (67/6404, 1000G_30x)
T=0.0112 (56/5008, 1000G)
T=0.0125 (56/4480, Estonian)
T=0.0065 (25/3854, ALSPAC)
T=0.0105 (39/3708, TWINSUK)
T=0.004 (4/998, GoNL)
T=0.032 (19/600, NorthernSweden)
T=0.006 (3/534, MGP)
C=0.5 (3/6, SGDP_PRJ)
T=0.5 (3/6, SGDP_PRJ)
C=0.5 (2/4, Siberian)
T=0.5 (2/4, 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	18890	C=0.99100	T=0.00900
European	Sub	14286	C=0.98908	T=0.01092
African	Sub	2946	C=0.9990	T=0.0010
African Others	Sub	114	C=1.000	T=0.000
African American	Sub	2832	C=0.9989	T=0.0011
Asian	Sub	112	C=1.000	T=0.000
East Asian	Sub	86	C=1.00	T=0.00
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=1.000	T=0.000
Latin American 2	Sub	610	C=1.000	T=0.000
South Asian	Sub	98	C=0.92	T=0.08
Other	Sub	692	C=0.996	T=0.004

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	C=0.994579	T=0.005421
gnomAD - Genomes	Global	Study-wide	140248	C=0.993811	T=0.006189
gnomAD - Genomes	European	Sub	75952	C=0.99059	T=0.00941
gnomAD - Genomes	African	Sub	42046	C=0.99862	T=0.00138
gnomAD - Genomes	American	Sub	13656	C=0.99487	T=0.00513
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9973	T=0.0027
gnomAD - Genomes	East Asian	Sub	3132	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2142	C=0.9925	T=0.0075
Allele Frequency Aggregator	Total	Global	18890	C=0.99100	T=0.00900
Allele Frequency Aggregator	European	Sub	14286	C=0.98908	T=0.01092
Allele Frequency Aggregator	African	Sub	2946	C=0.9990	T=0.0010
Allele Frequency Aggregator	Other	Sub	692	C=0.996	T=0.004
Allele Frequency Aggregator	Latin American 2	Sub	610	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	T=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.92	T=0.08
1000Genomes_30x	Global	Study-wide	6404	C=0.9895	T=0.0105
1000Genomes_30x	African	Sub	1786	C=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	C=0.9889	T=0.0111
1000Genomes_30x	South Asian	Sub	1202	C=0.9584	T=0.0416
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.997	T=0.003
1000Genomes	Global	Study-wide	5008	C=0.9888	T=0.0112
1000Genomes	African	Sub	1322	C=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9901	T=0.0099
1000Genomes	South Asian	Sub	978	C=0.955	T=0.045
1000Genomes	American	Sub	694	C=0.997	T=0.003
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9875	T=0.0125
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9935	T=0.0065
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9895	T=0.0105
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.996	T=0.004
Northern Sweden	ACPOP	Study-wide	600	C=0.968	T=0.032
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.994	T=0.006
SGDP_PRJ	Global	Study-wide	6	C=0.5	T=0.5
Siberian	Global	Study-wide	4	C=0.5	T=0.5

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.122058988C>T
GRCh37.p13 chr 12	NC_000012.11:g.122496894C>T
GRCh38.p14 chr 12 fix patch HG2247_PATCH	NW_011332697.1:g.1254C>T

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.562-104C… NM_001024808.3:c.562-104C>T	N/A	Intron Variant
BCL7A transcript variant 1	NM_020993.5:c.625-104C>T	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	C=	T
GRCh38.p14 chr 12	NC_000012.12:g.122058988=	NC_000012.12:g.122058988C>T
GRCh37.p13 chr 12	NC_000012.11:g.122496894=	NC_000012.11:g.122496894C>T
GRCh38.p14 chr 12 fix patch HG2247_PATCH	NW_011332697.1:g.1254=	NW_011332697.1:g.1254C>T
BCL7A transcript variant 2	NM_001024808.1:c.562-104=	NM_001024808.1:c.562-104C>T
BCL7A transcript variant 2	NM_001024808.3:c.562-104=	NM_001024808.3:c.562-104C>T
BCL7A transcript variant 1	NM_020993.3:c.625-104=	NM_020993.3:c.625-104C>T
BCL7A transcript variant 1	NM_020993.5:c.625-104=	NM_020993.5:c.625-104C>T

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#.

33 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss337667936	May 09, 2011 (134)
2	ILLUMINA	ss536282471	Sep 08, 2015 (146)
3	SSMP	ss659039932	Apr 25, 2013 (138)
4	WARNICH_LAB	ss678390581	Apr 25, 2013 (138)
5	EVA-GONL	ss990040601	Aug 21, 2014 (142)
6	JMKIDD_LAB	ss1078829901	Aug 21, 2014 (142)
7	1000GENOMES	ss1346951793	Aug 21, 2014 (142)
8	EVA_UK10K_ALSPAC	ss1629613067	Apr 01, 2015 (144)
9	EVA_DECODE	ss1642150549	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1672607100	Apr 01, 2015 (144)
11	EVA_MGP	ss1711346362	Apr 01, 2015 (144)
12	JJLAB	ss2027453770	Sep 14, 2016 (149)
13	USC_VALOUEV	ss2155809589	Dec 20, 2016 (150)
14	HUMAN_LONGEVITY	ss2193844611	Dec 20, 2016 (150)
15	GNOMAD	ss2916072840	Nov 08, 2017 (151)
16	SWEGEN	ss3010479038	Nov 08, 2017 (151)
17	CSHL	ss3350285851	Nov 08, 2017 (151)
18	ILLUMINA	ss3626988017	Oct 12, 2018 (152)
19	EGCUT_WGS	ss3677779448	Jul 13, 2019 (153)
20	EVA_DECODE	ss3694628805	Jul 13, 2019 (153)
21	ACPOP	ss3739451787	Jul 13, 2019 (153)
22	SGDP_PRJ	ss3879276797	Apr 27, 2020 (154)
23	EVA	ss3986590406	Apr 26, 2021 (155)
24	TOPMED	ss4935460573	Apr 26, 2021 (155)
25	1000G_HIGH_COVERAGE	ss5292514942	Oct 16, 2022 (156)
26	EVA	ss5408735503	Oct 16, 2022 (156)
27	HUGCELL_USP	ss5487090607	Oct 16, 2022 (156)
28	1000G_HIGH_COVERAGE	ss5590869996	Oct 16, 2022 (156)
29	SANFORD_IMAGENETICS	ss5654110854	Oct 16, 2022 (156)
30	EVA	ss5838622760	Oct 16, 2022 (156)
31	EVA	ss5848365682	Oct 16, 2022 (156)
32	EVA	ss5906340839	Oct 16, 2022 (156)
33	EVA	ss5945525315	Oct 16, 2022 (156)
34	1000Genomes	NC_000012.11 - 122496894	Oct 12, 2018 (152)
35	1000Genomes_30x	NC_000012.12 - 122058988	Oct 16, 2022 (156)
36	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 122496894	Oct 12, 2018 (152)
37	Genetic variation in the Estonian population	NC_000012.11 - 122496894	Oct 12, 2018 (152)
38	gnomAD - Genomes	NC_000012.12 - 122058988	Apr 26, 2021 (155)
39	Genome of the Netherlands Release 5	NC_000012.11 - 122496894	Apr 27, 2020 (154)
40	Medical Genome Project healthy controls from Spanish population	NC_000012.11 - 122496894	Apr 27, 2020 (154)
41	Northern Sweden	NC_000012.11 - 122496894	Jul 13, 2019 (153)
42	SGDP_PRJ	NC_000012.11 - 122496894	Apr 27, 2020 (154)
43	Siberian	NC_000012.11 - 122496894	Apr 27, 2020 (154)
44	TopMed	NC_000012.12 - 122058988	Apr 26, 2021 (155)
45	UK 10K study - Twins	NC_000012.11 - 122496894	Oct 12, 2018 (152)
46	ALFA	NC_000012.12 - 122058988	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1642150549	NC_000012.10:120981276:C:T	NC_000012.12:122058987:C:T	(self)
59774409, 33201767, 23517696, 14806187, 462122, 12736652, 31293777, 8325943, 33201767, ss337667936, ss536282471, ss659039932, ss678390581, ss990040601, ss1078829901, ss1346951793, ss1629613067, ss1672607100, ss1711346362, ss2027453770, ss2155809589, ss2916072840, ss3010479038, ss3350285851, ss3626988017, ss3677779448, ss3739451787, ss3879276797, ss3986590406, ss5408735503, ss5654110854, ss5838622760, ss5848365682, ss5945525315	NC_000012.11:122496893:C:T	NC_000012.12:122058987:C:T	(self)
78395931, 421628785, 151006230, 543336132, ss2193844611, ss3694628805, ss4935460573, ss5292514942, ss5487090607, ss5590869996, ss5906340839	NC_000012.12:122058987:C:T	NC_000012.12:122058987:C:T	(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 rs142704172

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

rs142704172