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dbSNP Short Genetic Variations

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.

rs141247767

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:147622159 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.005686 (1505/264690, TOPMED)
C=0.006318 (886/140244, GnomAD)
C=0.00740 (142/19190, ALFA) (+ 11 more)
C=0.0047 (30/6404, 1000G_30x)
C=0.0052 (26/5008, 1000G)
C=0.0074 (33/4480, Estonian)
C=0.0070 (27/3854, ALSPAC)
C=0.0108 (40/3708, TWINSUK)
C=0.008 (8/998, GoNL)
C=0.020 (12/600, NorthernSweden)
T=0.5 (3/6, SGDP_PRJ)
C=0.5 (3/6, SGDP_PRJ)
T=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)
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 19190 T=0.99260 C=0.00740
European Sub 14286 T=0.99111 C=0.00889
African Sub 2970 T=0.9983 C=0.0017
African Others Sub 114 T=1.000 C=0.000
African American Sub 2856 T=0.9982 C=0.0018
Asian Sub 116 T=1.000 C=0.000
East Asian Sub 88 T=1.00 C=0.00
Other Asian Sub 28 T=1.00 C=0.00
Latin American 1 Sub 154 T=1.000 C=0.000
Latin American 2 Sub 616 T=0.997 C=0.003
South Asian Sub 98 T=1.00 C=0.00
Other Sub 950 T=0.992 C=0.008


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 T=0.994314 C=0.005686
gnomAD - Genomes Global Study-wide 140244 T=0.993682 C=0.006318
gnomAD - Genomes European Sub 75954 T=0.99140 C=0.00860
gnomAD - Genomes African Sub 42030 T=0.99845 C=0.00155
gnomAD - Genomes American Sub 13650 T=0.99429 C=0.00571
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9786 C=0.0214
gnomAD - Genomes East Asian Sub 3134 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2152 T=0.9912 C=0.0088
Allele Frequency Aggregator Total Global 19190 T=0.99260 C=0.00740
Allele Frequency Aggregator European Sub 14286 T=0.99111 C=0.00889
Allele Frequency Aggregator African Sub 2970 T=0.9983 C=0.0017
Allele Frequency Aggregator Other Sub 950 T=0.992 C=0.008
Allele Frequency Aggregator Latin American 2 Sub 616 T=0.997 C=0.003
Allele Frequency Aggregator Latin American 1 Sub 154 T=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 116 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 T=1.00 C=0.00
1000Genomes_30x Global Study-wide 6404 T=0.9953 C=0.0047
1000Genomes_30x African Sub 1786 T=1.0000 C=0.0000
1000Genomes_30x Europe Sub 1266 T=0.9905 C=0.0095
1000Genomes_30x South Asian Sub 1202 T=0.9867 C=0.0133
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=0.998 C=0.002
1000Genomes Global Study-wide 5008 T=0.9948 C=0.0052
1000Genomes African Sub 1322 T=1.0000 C=0.0000
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=0.9901 C=0.0099
1000Genomes South Asian Sub 978 T=0.986 C=0.014
1000Genomes American Sub 694 T=0.997 C=0.003
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9926 C=0.0074
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9930 C=0.0070
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9892 C=0.0108
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.992 C=0.008
Northern Sweden ACPOP Study-wide 600 T=0.980 C=0.020
SGDP_PRJ Global Study-wide 6 T=0.5 C=0.5
Siberian Global Study-wide 2 T=0.5 C=0.5
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 1 NC_000001.11:g.147622159T>C
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.4437572T>C
GRCh37.p13 chr 1 NC_000001.10:g.147093960T>C
Gene: BCL9, BCL9 transcription coactivator (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BCL9 transcript NM_004326.4:c.2903-112T>C 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 T= C
GRCh38.p14 chr 1 NC_000001.11:g.147622159= NC_000001.11:g.147622159T>C
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.4437572= NW_003871055.3:g.4437572T>C
GRCh37.p13 chr 1 NC_000001.10:g.147093960= NC_000001.10:g.147093960T>C
BCL9 transcript NM_004326.3:c.2903-112= NM_004326.3:c.2903-112T>C
BCL9 transcript NM_004326.4:c.2903-112= NM_004326.4:c.2903-112T>C
BCL9 transcript variant X1 XM_005272971.1:c.2903-112= XM_005272971.1:c.2903-112T>C
BCL9 transcript variant X2 XM_005272972.1:c.2903-112= XM_005272972.1:c.2903-112T>C
BCL9 transcript variant X3 XM_005272973.1:c.2681-112= XM_005272973.1:c.2681-112T>C
BCL9 transcript variant X1 XM_005277416.1:c.2903-112= XM_005277416.1:c.2903-112T>C
BCL9 transcript variant X2 XM_005277417.1:c.2903-112= XM_005277417.1:c.2903-112T>C
BCL9 transcript variant X3 XM_005277418.1:c.2681-112= XM_005277418.1:c.2681-112T>C
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#.

25 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss328921378 May 09, 2011 (134)
2 ILLUMINA ss536466870 Sep 11, 2015 (146)
3 EVA-GONL ss975645727 Apr 09, 2015 (144)
4 1000GENOMES ss1292762251 Aug 28, 2014 (142)
5 EVA_UK10K_ALSPAC ss1601138625 Apr 09, 2015 (144)
6 EVA_UK10K_TWINSUK ss1644132658 Apr 09, 2015 (144)
7 JJLAB ss2019953868 Sep 28, 2016 (149)
8 USC_VALOUEV ss2147976932 Oct 11, 2018 (152)
9 HUMAN_LONGEVITY ss2166264753 Dec 20, 2016 (150)
10 GNOMAD ss2760730748 Oct 11, 2018 (152)
11 SWEGEN ss2987659079 Oct 11, 2018 (152)
12 ILLUMINA ss3626199345 Oct 11, 2018 (152)
13 EGCUT_WGS ss3655638162 Jul 12, 2019 (153)
14 ACPOP ss3727454133 Jul 12, 2019 (153)
15 KHV_HUMAN_GENOMES ss3799765768 Jul 12, 2019 (153)
16 SGDP_PRJ ss3849893053 Apr 25, 2020 (154)
17 GNOMAD ss4002747491 Apr 25, 2021 (155)
18 TOPMED ss4466788240 Apr 25, 2021 (155)
19 1000G_HIGH_COVERAGE ss5244132792 Oct 12, 2022 (156)
20 EVA ss5321758050 Oct 12, 2022 (156)
21 HUGCELL_USP ss5444773413 Oct 12, 2022 (156)
22 1000G_HIGH_COVERAGE ss5517382212 Oct 12, 2022 (156)
23 EVA ss5832605479 Oct 12, 2022 (156)
24 EVA ss5910102381 Oct 12, 2022 (156)
25 EVA ss5938310220 Oct 12, 2022 (156)
26 1000Genomes NC_000001.10 - 147093960 Oct 11, 2018 (152)
27 1000Genomes_30x NC_000001.11 - 147622159 Oct 12, 2022 (156)
28 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 147093960 Oct 11, 2018 (152)
29 Genetic variation in the Estonian population NC_000001.10 - 147093960 Oct 11, 2018 (152)
30 gnomAD - Genomes NC_000001.11 - 147622159 Apr 25, 2021 (155)
31 Genome of the Netherlands Release 5 NC_000001.10 - 147093960 Apr 25, 2020 (154)
32 Northern Sweden NC_000001.10 - 147093960 Jul 12, 2019 (153)
33 SGDP_PRJ NC_000001.10 - 147093960 Apr 25, 2020 (154)
34 Siberian NC_000001.10 - 147093960 Apr 25, 2020 (154)
35 TopMed NC_000001.11 - 147622159 Apr 25, 2021 (155)
36 UK 10K study - Twins NC_000001.10 - 147093960 Oct 11, 2018 (152)
37 ALFA NC_000001.11 - 147622159 Apr 25, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
3548512, 1937311, 1376410, 843792, 738998, 1910033, 493286, 1937311, ss328921378, ss536466870, ss975645727, ss1292762251, ss1601138625, ss1644132658, ss2019953868, ss2147976932, ss2760730748, ss2987659079, ss3626199345, ss3655638162, ss3727454133, ss3849893053, ss5321758050, ss5832605479, ss5938310220 NC_000001.10:147093959:T:C NC_000001.11:147622158:T:C (self)
4908147, 25727756, 30394575, 9108362358, ss2166264753, ss3799765768, ss4002747491, ss4466788240, ss5244132792, ss5444773413, ss5517382212, ss5910102381 NC_000001.11:147622158:T:C NC_000001.11:147622158:T:C (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 rs141247767

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