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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs2272148

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:187731681 (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=0.005108 (1352/264690, TOPMED)
T=0.005677 (1409/248176, GnomAD_exome)
T=0.004232 (593/140136, GnomAD) (+ 20 more)
T=0.005799 (683/117774, ExAC)
T=0.00297 (87/29332, ALFA)
T=0.01893 (535/28258, 14KJPN)
T=0.01951 (327/16760, 8.3KJPN)
T=0.00469 (61/13006, GO-ESP)
T=0.0041 (26/6404, 1000G_30x)
T=0.0044 (22/5008, 1000G)
T=0.0013 (6/4480, Estonian)
T=0.0049 (19/3854, ALSPAC)
T=0.0084 (31/3708, TWINSUK)
T=0.0266 (78/2930, KOREAN)
T=0.0246 (45/1832, Korea1K)
T=0.0044 (5/1136, Daghestan)
T=0.004 (4/998, GoNL)
T=0.005 (3/600, NorthernSweden)
T=0.004 (2/534, MGP)
T=0.019 (9/474, HapMap)
T=0.014 (3/210, Vietnamese)
C=0.50 (6/12, SGDP_PRJ)
T=0.50 (6/12, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BCL6 : Intron Variant
LOC100131635 : 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 29332 C=0.99703 T=0.00297
European Sub 20356 C=0.99691 T=0.00309
African Sub 4678 C=0.9998 T=0.0002
African Others Sub 152 C=1.000 T=0.000
African American Sub 4526 C=0.9998 T=0.0002
Asian Sub 172 C=1.000 T=0.000
East Asian Sub 114 C=1.000 T=0.000
Other Asian Sub 58 C=1.00 T=0.00
Latin American 1 Sub 154 C=0.994 T=0.006
Latin American 2 Sub 616 C=0.994 T=0.006
South Asian Sub 98 C=1.00 T=0.00
Other Sub 3258 C=0.9945 T=0.0055


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.994892 T=0.005108
gnomAD - Exomes Global Study-wide 248176 C=0.994323 T=0.005677
gnomAD - Exomes European Sub 132766 C=0.995353 T=0.004647
gnomAD - Exomes Asian Sub 48866 C=0.99271 T=0.00729
gnomAD - Exomes American Sub 34442 C=0.98853 T=0.01147
gnomAD - Exomes African Sub 16052 C=0.99907 T=0.00093
gnomAD - Exomes Ashkenazi Jewish Sub 9978 C=0.9999 T=0.0001
gnomAD - Exomes Other Sub 6072 C=0.9959 T=0.0041
gnomAD - Genomes Global Study-wide 140136 C=0.995768 T=0.004232
gnomAD - Genomes European Sub 75896 C=0.99498 T=0.00502
gnomAD - Genomes African Sub 41982 C=0.99857 T=0.00143
gnomAD - Genomes American Sub 13652 C=0.99216 T=0.00784
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3130 C=0.9875 T=0.0125
gnomAD - Genomes Other Sub 2154 C=0.9972 T=0.0028
ExAC Global Study-wide 117774 C=0.994201 T=0.005799
ExAC Europe Sub 71490 C=0.99530 T=0.00470
ExAC Asian Sub 24504 C=0.99229 T=0.00771
ExAC American Sub 11228 C=0.98762 T=0.01238
ExAC African Sub 9678 C=0.9987 T=0.0013
ExAC Other Sub 874 C=0.993 T=0.007
Allele Frequency Aggregator Total Global 29332 C=0.99703 T=0.00297
Allele Frequency Aggregator European Sub 20356 C=0.99691 T=0.00309
Allele Frequency Aggregator African Sub 4678 C=0.9998 T=0.0002
Allele Frequency Aggregator Other Sub 3258 C=0.9945 T=0.0055
Allele Frequency Aggregator Latin American 2 Sub 616 C=0.994 T=0.006
Allele Frequency Aggregator Asian Sub 172 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 154 C=0.994 T=0.006
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
14KJPN JAPANESE Study-wide 28258 C=0.98107 T=0.01893
8.3KJPN JAPANESE Study-wide 16760 C=0.98049 T=0.01951
GO Exome Sequencing Project Global Study-wide 13006 C=0.99531 T=0.00469
GO Exome Sequencing Project European American Sub 8600 C=0.9934 T=0.0066
GO Exome Sequencing Project African American Sub 4406 C=0.9991 T=0.0009
1000Genomes_30x Global Study-wide 6404 C=0.9959 T=0.0041
1000Genomes_30x African Sub 1786 C=0.9989 T=0.0011
1000Genomes_30x Europe Sub 1266 C=0.9968 T=0.0032
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=0.9872 T=0.0128
1000Genomes_30x American Sub 980 C=0.995 T=0.005
1000Genomes Global Study-wide 5008 C=0.9956 T=0.0044
1000Genomes African Sub 1322 C=0.9985 T=0.0015
1000Genomes East Asian Sub 1008 C=0.9861 T=0.0139
1000Genomes Europe Sub 1006 C=0.9970 T=0.0030
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.996 T=0.004
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9987 T=0.0013
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9951 T=0.0049
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9916 T=0.0084
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.9734 T=0.0266
Korean Genome Project KOREAN Study-wide 1832 C=0.9754 T=0.0246
Genome-wide autozygosity in Daghestan Global Study-wide 1136 C=0.9956 T=0.0044
Genome-wide autozygosity in Daghestan Daghestan Sub 628 C=0.997 T=0.003
Genome-wide autozygosity in Daghestan Near_East Sub 144 C=0.993 T=0.007
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.984 T=0.016
Genome-wide autozygosity in Daghestan Europe Sub 108 C=1.000 T=0.000
Genome-wide autozygosity in Daghestan South Asian Sub 98 C=1.00 T=0.00
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=1.00 T=0.00
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=0.995 T=0.005
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.996 T=0.004
HapMap Global Study-wide 474 C=0.981 T=0.019
HapMap Asian Sub 254 C=0.972 T=0.028
HapMap African Sub 120 C=1.000 T=0.000
HapMap American Sub 100 C=0.98 T=0.02
A Vietnamese Genetic Variation Database Global Study-wide 210 C=0.986 T=0.014
SGDP_PRJ Global Study-wide 12 C=0.50 T=0.50
Help

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 3 NC_000003.12:g.187731681C>T
GRCh37.p13 chr 3 NC_000003.11:g.187449469C>T
BCL6 RefSeqGene NG_007149.1:g.18855G>A
Gene: BCL6, BCL6 transcription repressor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
BCL6 transcript variant 2 NM_001130845.2:c.383+28G>A N/A Intron Variant
BCL6 transcript variant 3 NM_001134738.1:c.383+28G>A N/A Intron Variant
BCL6 transcript variant 1 NM_001706.5:c.383+28G>A N/A Intron Variant
BCL6 transcript variant X1 XM_005247694.5:c.383+28G>A N/A Intron Variant
BCL6 transcript variant X3 XM_011513062.4:c.383+28G>A N/A Intron Variant
BCL6 transcript variant X2 XM_047448655.1:c.383+28G>A N/A Intron Variant
Gene: LOC100131635, hCG1645011-like (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC100131635 transcript NR_034062.1:n. N/A Intron Variant
Help

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
Help

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 3 NC_000003.12:g.187731681= NC_000003.12:g.187731681C>T
GRCh37.p13 chr 3 NC_000003.11:g.187449469= NC_000003.11:g.187449469C>T
BCL6 RefSeqGene NG_007149.1:g.18855= NG_007149.1:g.18855G>A
BCL6 transcript variant 2 NM_001130845.1:c.383+28= NM_001130845.1:c.383+28G>A
BCL6 transcript variant 2 NM_001130845.2:c.383+28= NM_001130845.2:c.383+28G>A
BCL6 transcript variant 3 NM_001134738.1:c.383+28= NM_001134738.1:c.383+28G>A
BCL6 transcript variant 1 NM_001706.4:c.383+28= NM_001706.4:c.383+28G>A
BCL6 transcript variant 1 NM_001706.5:c.383+28= NM_001706.5:c.383+28G>A
BCL6 transcript variant X1 XM_005247694.1:c.383+28= XM_005247694.1:c.383+28G>A
BCL6 transcript variant X1 XM_005247694.5:c.383+28= XM_005247694.5:c.383+28G>A
BCL6 transcript variant X3 XM_011513062.4:c.383+28= XM_011513062.4:c.383+28G>A
BCL6 transcript variant X2 XM_047448655.1:c.383+28= XM_047448655.1:c.383+28G>A
Help

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#.

51 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3207177 Sep 28, 2001 (100)
2 ILLUMINA ss75100852 Dec 07, 2007 (129)
3 KRIBB_YJKIM ss119425619 Dec 01, 2009 (131)
4 ILLUMINA ss173232491 Jul 04, 2010 (132)
5 1000GENOMES ss331314183 May 09, 2011 (134)
6 1000GENOMES ss490880188 May 04, 2012 (137)
7 ILLUMINA ss537066049 Sep 08, 2015 (146)
8 NHLBI-ESP ss712572965 Apr 25, 2013 (138)
9 EVA-GONL ss979571697 Aug 21, 2014 (142)
10 JMKIDD_LAB ss1071141956 Aug 21, 2014 (142)
11 1000GENOMES ss1307716930 Aug 21, 2014 (142)
12 HAMMER_LAB ss1397362601 Sep 08, 2015 (146)
13 EVA_DECODE ss1589070258 Apr 01, 2015 (144)
14 EVA_UK10K_ALSPAC ss1609042471 Apr 01, 2015 (144)
15 EVA_UK10K_TWINSUK ss1652036504 Apr 01, 2015 (144)
16 EVA_EXAC ss1687336730 Apr 01, 2015 (144)
17 EVA_MGP ss1711044472 Apr 01, 2015 (144)
18 EVA_SVP ss1712639341 Apr 01, 2015 (144)
19 JJLAB ss2021972088 Sep 14, 2016 (149)
20 HUMAN_LONGEVITY ss2259097601 Dec 20, 2016 (150)
21 SYSTEMSBIOZJU ss2625485357 Nov 08, 2017 (151)
22 GRF ss2705497343 Nov 08, 2017 (151)
23 GNOMAD ss2734267468 Nov 08, 2017 (151)
24 GNOMAD ss2747159358 Nov 08, 2017 (151)
25 GNOMAD ss2803612417 Nov 08, 2017 (151)
26 SWEGEN ss2993821221 Nov 08, 2017 (151)
27 ILLUMINA ss3628861340 Oct 12, 2018 (152)
28 ILLUMINA ss3638462643 Oct 12, 2018 (152)
29 ILLUMINA ss3643415840 Oct 12, 2018 (152)
30 EGCUT_WGS ss3661779884 Jul 13, 2019 (153)
31 EVA_DECODE ss3711047249 Jul 13, 2019 (153)
32 ACPOP ss3730689563 Jul 13, 2019 (153)
33 EVA ss3761168567 Jul 13, 2019 (153)
34 KHV_HUMAN_GENOMES ss3804305492 Jul 13, 2019 (153)
35 EVA ss3823983493 Apr 25, 2020 (154)
36 SGDP_PRJ ss3857798011 Apr 25, 2020 (154)
37 KRGDB ss3903891234 Apr 25, 2020 (154)
38 KOGIC ss3953161454 Apr 25, 2020 (154)
39 EVA ss3986265308 Apr 26, 2021 (155)
40 EVA ss4017124680 Apr 26, 2021 (155)
41 TOPMED ss4597233340 Apr 26, 2021 (155)
42 TOMMO_GENOMICS ss5163354935 Apr 26, 2021 (155)
43 1000G_HIGH_COVERAGE ss5257395042 Oct 13, 2022 (156)
44 EVA ss5345767674 Oct 13, 2022 (156)
45 HUGCELL_USP ss5456402317 Oct 13, 2022 (156)
46 1000G_HIGH_COVERAGE ss5537548825 Oct 13, 2022 (156)
47 SANFORD_IMAGENETICS ss5633970693 Oct 13, 2022 (156)
48 TOMMO_GENOMICS ss5696744597 Oct 13, 2022 (156)
49 YY_MCH ss5804583268 Oct 13, 2022 (156)
50 EVA ss5872569401 Oct 13, 2022 (156)
51 EVA ss5962354973 Oct 13, 2022 (156)
52 1000Genomes NC_000003.11 - 187449469 Oct 12, 2018 (152)
53 1000Genomes_30x NC_000003.12 - 187731681 Oct 13, 2022 (156)
54 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 187449469 Oct 12, 2018 (152)
55 Genome-wide autozygosity in Daghestan NC_000003.10 - 188932163 Apr 25, 2020 (154)
56 Genetic variation in the Estonian population NC_000003.11 - 187449469 Oct 12, 2018 (152)
57 ExAC NC_000003.11 - 187449469 Oct 12, 2018 (152)
58 gnomAD - Genomes NC_000003.12 - 187731681 Apr 26, 2021 (155)
59 gnomAD - Exomes NC_000003.11 - 187449469 Jul 13, 2019 (153)
60 GO Exome Sequencing Project NC_000003.11 - 187449469 Oct 12, 2018 (152)
61 Genome of the Netherlands Release 5 NC_000003.11 - 187449469 Apr 25, 2020 (154)
62 HapMap NC_000003.12 - 187731681 Apr 25, 2020 (154)
63 KOREAN population from KRGDB NC_000003.11 - 187449469 Apr 25, 2020 (154)
64 Korean Genome Project NC_000003.12 - 187731681 Apr 25, 2020 (154)
65 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 187449469 Apr 25, 2020 (154)
66 Northern Sweden NC_000003.11 - 187449469 Jul 13, 2019 (153)
67 SGDP_PRJ NC_000003.11 - 187449469 Apr 25, 2020 (154)
68 8.3KJPN NC_000003.11 - 187449469 Apr 26, 2021 (155)
69 14KJPN NC_000003.12 - 187731681 Oct 13, 2022 (156)
70 TopMed NC_000003.12 - 187731681 Apr 26, 2021 (155)
71 UK 10K study - Twins NC_000003.11 - 187449469 Oct 12, 2018 (152)
72 A Vietnamese Genetic Variation Database NC_000003.11 - 187449469 Jul 13, 2019 (153)
73 ALFA NC_000003.12 - 187731681 Apr 26, 2021 (155)
Help

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)
rs386563109 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
338288, ss1397362601, ss1589070258, ss1712639341, ss3643415840 NC_000003.10:188932162:C:T NC_000003.12:187731680:C:T (self)
19040745, 10614464, 7518132, 7287183, 3362671, 441760, 4662814, 11068628, 160232, 3974428, 9814991, 21324242, 10614464, 2319995, ss331314183, ss490880188, ss537066049, ss712572965, ss979571697, ss1071141956, ss1307716930, ss1609042471, ss1652036504, ss1687336730, ss1711044472, ss2021972088, ss2625485357, ss2705497343, ss2734267468, ss2747159358, ss2803612417, ss2993821221, ss3628861340, ss3638462643, ss3661779884, ss3730689563, ss3761168567, ss3823983493, ss3857798011, ss3903891234, ss3986265308, ss4017124680, ss5163354935, ss5345767674, ss5633970693, ss5962354973 NC_000003.11:187449468:C:T NC_000003.12:187731680:C:T (self)
25074760, 135255360, 2529307, 9539455, 30581701, 434610895, 6744293937, ss2259097601, ss3711047249, ss3804305492, ss3953161454, ss4597233340, ss5257395042, ss5456402317, ss5537548825, ss5696744597, ss5804583268, ss5872569401 NC_000003.12:187731680:C:T NC_000003.12:187731680:C:T (self)
ss3207177, ss75100852, ss119425619, ss173232491 NT_005612.16:93944614:C:T NC_000003.12:187731680:C:T (self)
Help

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

No publications for rs2272148

Help

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.

Software version is: 2.0.1.post761+d5e8e07