Name: rs3970
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.

rs3970

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:33594148 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.113480 (30037/264690, TOPMED)
A=0.095425 (13377/140184, GnomAD)
A=0.03690 (1115/30220, ALFA) (+ 14 more)
A=0.03528 (997/28258, 14KJPN)
A=0.03562 (597/16760, 8.3KJPN)
A=0.1301 (833/6404, 1000G_30x)
A=0.1222 (612/5008, 1000G)
A=0.0002 (1/4480, Estonian)
A=0.0005 (2/3854, ALSPAC)
A=0.0013 (5/3708, TWINSUK)
A=0.0406 (119/2930, KOREAN)
A=0.0349 (64/1832, Korea1K)
A=0.126 (41/326, HapMap)
A=0.097 (21/216, Qatari)
G=0.40 (34/84, SGDP_PRJ)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CBFA2T2 : 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	30220	G=0.96310	A=0.03690
European	Sub	24736	G=0.99838	A=0.00162
African	Sub	3168	G=0.7478	A=0.2522
African Others	Sub	124	G=0.685	A=0.315
African American	Sub	3044	G=0.7503	A=0.2497
Asian	Sub	128	G=0.977	A=0.023
East Asian	Sub	100	G=0.97	A=0.03
Other Asian	Sub	28	G=1.00	A=0.00
Latin American 1	Sub	168	G=0.905	A=0.095
Latin American 2	Sub	700	G=0.769	A=0.231
South Asian	Sub	114	G=0.965	A=0.035
Other	Sub	1206	G=0.9245	A=0.0755

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=0.886520	A=0.113480
gnomAD - Genomes	Global	Study-wide	140184	G=0.904575	A=0.095425
gnomAD - Genomes	European	Sub	75962	G=0.99867	A=0.00133
gnomAD - Genomes	African	Sub	41966	G=0.74548	A=0.25452
gnomAD - Genomes	American	Sub	13652	G=0.83197	A=0.16803
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.9994	A=0.0006
gnomAD - Genomes	East Asian	Sub	3130	G=0.9661	A=0.0339
gnomAD - Genomes	Other	Sub	2150	G=0.9102	A=0.0898
Allele Frequency Aggregator	Total	Global	30220	G=0.96310	A=0.03690
Allele Frequency Aggregator	European	Sub	24736	G=0.99838	A=0.00162
Allele Frequency Aggregator	African	Sub	3168	G=0.7478	A=0.2522
Allele Frequency Aggregator	Other	Sub	1206	G=0.9245	A=0.0755
Allele Frequency Aggregator	Latin American 2	Sub	700	G=0.769	A=0.231
Allele Frequency Aggregator	Latin American 1	Sub	168	G=0.905	A=0.095
Allele Frequency Aggregator	Asian	Sub	128	G=0.977	A=0.023
Allele Frequency Aggregator	South Asian	Sub	114	G=0.965	A=0.035
14KJPN	JAPANESE	Study-wide	28258	G=0.96472	A=0.03528
8.3KJPN	JAPANESE	Study-wide	16760	G=0.96438	A=0.03562
1000Genomes_30x	Global	Study-wide	6404	G=0.8699	A=0.1301
1000Genomes_30x	African	Sub	1786	G=0.6887	A=0.3113
1000Genomes_30x	Europe	Sub	1266	G=1.0000	A=0.0000
1000Genomes_30x	South Asian	Sub	1202	G=0.9725	A=0.0275
1000Genomes_30x	East Asian	Sub	1170	G=0.9573	A=0.0427
1000Genomes_30x	American	Sub	980	G=0.802	A=0.198
1000Genomes	Global	Study-wide	5008	G=0.8778	A=0.1222
1000Genomes	African	Sub	1322	G=0.6921	A=0.3079
1000Genomes	East Asian	Sub	1008	G=0.9613	A=0.0387
1000Genomes	Europe	Sub	1006	G=1.0000	A=0.0000
1000Genomes	South Asian	Sub	978	G=0.969	A=0.031
1000Genomes	American	Sub	694	G=0.804	A=0.196
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9998	A=0.0002
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9995	A=0.0005
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9987	A=0.0013
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.9594	A=0.0406
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9651	A=0.0349
HapMap	Global	Study-wide	326	G=0.874	A=0.126
HapMap	American	Sub	120	G=1.000	A=0.000
HapMap	African	Sub	118	G=0.695	A=0.305
HapMap	Asian	Sub	88	G=0.94	A=0.06
Qatari	Global	Study-wide	216	G=0.903	A=0.097
SGDP_PRJ	Global	Study-wide	84	G=0.40	A=0.60
Siberian	Global	Study-wide	2	G=0.5	A=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 20	NC_000020.11:g.33594148G>A
GRCh37.p13 chr 20	NC_000020.10:g.32181954G>A

Gene: CBFA2T2, CBFA2/RUNX1 partner transcriptional co-repressor 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CBFA2T2 transcript variant 3	NM_001032999.3:c.35-12808… NM_001032999.3:c.35-12808G>A	N/A	Intron Variant
CBFA2T2 transcript variant 4	NM_001039709.2:c.-26-1280… NM_001039709.2:c.-26-12808G>A	N/A	Intron Variant
CBFA2T2 transcript variant 2	NM_005093.4:c.62-12808G>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
GRCh38.p14 chr 20	NC_000020.11:g.33594148=	NC_000020.11:g.33594148G>A
GRCh37.p13 chr 20	NC_000020.10:g.32181954=	NC_000020.10:g.32181954G>A
CBFA2T2 transcript variant 3	NM_001032999.2:c.35-12808=	NM_001032999.2:c.35-12808G>A
CBFA2T2 transcript variant 3	NM_001032999.3:c.35-12808=	NM_001032999.3:c.35-12808G>A
CBFA2T2 transcript variant 4	NM_001039709.1:c.-26-12808=	NM_001039709.1:c.-26-12808G>A
CBFA2T2 transcript variant 4	NM_001039709.2:c.-26-12808=	NM_001039709.2:c.-26-12808G>A
CBFA2T2 transcript variant 2	NM_005093.3:c.62-12808=	NM_005093.3:c.62-12808G>A
CBFA2T2 transcript variant 2	NM_005093.4:c.62-12808=	NM_005093.4:c.62-12808G>A
CBFA2T2 transcript variant X2	XM_005260615.1:c.62-12808=	XM_005260615.1:c.62-12808G>A

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#.

54 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SHGC/AFFYMETRIX	ss4009	Sep 19, 2000 (36)
2	WI_SSAHASNP	ss6788042	Feb 20, 2003 (123)
3	WI_SSAHASNP	ss11194524	Jul 11, 2003 (117)
4	KRIBB_YJKIM	ss104796537	Feb 03, 2009 (130)
5	1000GENOMES	ss113279528	Jan 25, 2009 (130)
6	COMPLETE_GENOMICS	ss169489289	Jul 04, 2010 (132)
7	BUSHMAN	ss203876210	Jul 04, 2010 (132)
8	1000GENOMES	ss228332256	Jul 14, 2010 (132)
9	1000GENOMES	ss243991850	Jul 15, 2010 (132)
10	GMI	ss283366786	May 04, 2012 (137)
11	ILLUMINA	ss481849362	May 04, 2012 (137)
12	ILLUMINA	ss484180358	May 04, 2012 (137)
13	ILLUMINA	ss534413181	Sep 08, 2015 (146)
14	TISHKOFF	ss566222451	Apr 25, 2013 (138)
15	SSMP	ss662104642	Apr 25, 2013 (138)
16	ILLUMINA	ss779921398	Sep 08, 2015 (146)
17	ILLUMINA	ss781584518	Sep 08, 2015 (146)
18	ILLUMINA	ss835399618	Sep 08, 2015 (146)
19	JMKIDD_LAB	ss1082175846	Aug 21, 2014 (142)
20	1000GENOMES	ss1364609189	Aug 21, 2014 (142)
21	EVA_UK10K_ALSPAC	ss1638693789	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1681687822	Apr 01, 2015 (144)
23	HAMMER_LAB	ss1809484545	Sep 08, 2015 (146)
24	WEILL_CORNELL_DGM	ss1938193639	Feb 12, 2016 (147)
25	GENOMED	ss1969125795	Jul 19, 2016 (147)
26	JJLAB	ss2029879347	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2158443181	Dec 20, 2016 (150)
28	HUMAN_LONGEVITY	ss2242409773	Dec 20, 2016 (150)
29	ILLUMINA	ss2633793065	Nov 08, 2017 (151)
30	GRF	ss2704133055	Nov 08, 2017 (151)
31	GNOMAD	ss2966950628	Nov 08, 2017 (151)
32	ILLUMINA	ss3628381510	Oct 12, 2018 (152)
33	ILLUMINA	ss3631749935	Oct 12, 2018 (152)
34	ILLUMINA	ss3642179669	Oct 12, 2018 (152)
35	EGCUT_WGS	ss3684799902	Jul 13, 2019 (153)
36	EVA	ss3758592631	Jul 13, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3821762295	Jul 13, 2019 (153)
38	SGDP_PRJ	ss3889020408	Apr 27, 2020 (154)
39	KRGDB	ss3939289388	Apr 27, 2020 (154)
40	KOGIC	ss3982197341	Apr 27, 2020 (154)
41	TOPMED	ss5087165804	Apr 26, 2021 (155)
42	TOMMO_GENOMICS	ss5229456086	Apr 26, 2021 (155)
43	1000G_HIGH_COVERAGE	ss5308656532	Oct 16, 2022 (156)
44	EVA	ss5316004628	Oct 16, 2022 (156)
45	EVA	ss5437139809	Oct 16, 2022 (156)
46	HUGCELL_USP	ss5500947647	Oct 16, 2022 (156)
47	EVA	ss5512204534	Oct 16, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5615047284	Oct 16, 2022 (156)
49	SANFORD_IMAGENETICS	ss5663138609	Oct 16, 2022 (156)
50	TOMMO_GENOMICS	ss5789194562	Oct 16, 2022 (156)
51	YY_MCH	ss5818013005	Oct 16, 2022 (156)
52	EVA	ss5853125669	Oct 16, 2022 (156)
53	EVA	ss5923262342	Oct 16, 2022 (156)
54	EVA	ss5958047204	Oct 16, 2022 (156)
55	1000Genomes	NC_000020.10 - 32181954	Oct 12, 2018 (152)
56	1000Genomes_30x	NC_000020.11 - 33594148	Oct 16, 2022 (156)
57	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 32181954	Oct 12, 2018 (152)
58	Genetic variation in the Estonian population	NC_000020.10 - 32181954	Oct 12, 2018 (152)
59	gnomAD - Genomes	NC_000020.11 - 33594148	Apr 26, 2021 (155)
60	HapMap	NC_000020.11 - 33594148	Apr 27, 2020 (154)
61	KOREAN population from KRGDB	NC_000020.10 - 32181954	Apr 27, 2020 (154)
62	Korean Genome Project	NC_000020.11 - 33594148	Apr 27, 2020 (154)
63	Qatari	NC_000020.10 - 32181954	Apr 27, 2020 (154)
64	SGDP_PRJ	NC_000020.10 - 32181954	Apr 27, 2020 (154)
65	Siberian	NC_000020.10 - 32181954	Apr 27, 2020 (154)
66	8.3KJPN	NC_000020.10 - 32181954	Apr 26, 2021 (155)
67	14KJPN	NC_000020.11 - 33594148	Oct 16, 2022 (156)
68	TopMed	NC_000020.11 - 33594148	Apr 26, 2021 (155)
69	UK 10K study - Twins	NC_000020.10 - 32181954	Oct 12, 2018 (152)
70	ALFA	NC_000020.11 - 33594148	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)
rs4911349	Sep 24, 2004 (123)
rs7409641	Aug 27, 2003 (117)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss113279528, ss169489289, ss203876210, ss283366786, ss484180358	NC_000020.9:31645614:G:A	NC_000020.11:33594147:G:A	(self)
78066839, 43212891, 30538150, 46466782, 20235561, 41037388, 10959535, 87425393, 43212891, ss228332256, ss243991850, ss481849362, ss534413181, ss566222451, ss662104642, ss779921398, ss781584518, ss835399618, ss1082175846, ss1364609189, ss1638693789, ss1681687822, ss1809484545, ss1938193639, ss1969125795, ss2029879347, ss2158443181, ss2633793065, ss2704133055, ss2966950628, ss3628381510, ss3631749935, ss3642179669, ss3684799902, ss3758592631, ss3889020408, ss3939289388, ss5229456086, ss5316004628, ss5437139809, ss5512204534, ss5663138609, ss5958047204	NC_000020.10:32181953:G:A	NC_000020.11:33594147:G:A	(self)
102573219, 550652629, 2109849, 38575342, 123031666, 362274749, 1782527038, ss2242409773, ss3821762295, ss3982197341, ss5087165804, ss5308656532, ss5500947647, ss5615047284, ss5789194562, ss5818013005, ss5853125669, ss5923262342	NC_000020.11:33594147:G:A	NC_000020.11:33594147:G:A	(self)
ss4009, ss104796537	NT_011362.10:2378045:G:A	NC_000020.11:33594147:G:A	(self)
ss6788042, ss11194524	NT_028392.4:2348721:G:A	NC_000020.11:33594147:G: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 rs3970

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

rs3970