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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.

rs200837308

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:85267844 (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=0.000144 (38/264690, TOPMED)
A=0.000235 (59/251460, GnomAD_exome)
A=0.000086 (12/140252, GnomAD) (+ 9 more)
A=0.000214 (26/121394, ExAC)
A=0.00142 (112/78698, PAGE_STUDY)
A=0.00009 (4/45080, ALFA)
A=0.01883 (532/28258, 14KJPN)
A=0.01885 (316/16760, 8.3KJPN)
A=0.0003 (2/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)
A=0.0062 (18/2922, KOREAN)
A=0.0049 (9/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BCL10 : Missense 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 45080 G=0.99991 A=0.00009
European Sub 32728 G=0.99994 A=0.00006
African Sub 3946 G=1.0000 A=0.0000
African Others Sub 122 G=1.000 A=0.000
African American Sub 3824 G=1.0000 A=0.0000
Asian Sub 202 G=1.000 A=0.000
East Asian Sub 146 G=1.000 A=0.000
Other Asian Sub 56 G=1.00 A=0.00
Latin American 1 Sub 500 G=1.000 A=0.000
Latin American 2 Sub 628 G=1.000 A=0.000
South Asian Sub 104 G=1.000 A=0.000
Other Sub 6972 G=0.9997 A=0.0003


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 G=0.999856 A=0.000144
gnomAD - Exomes Global Study-wide 251460 G=0.999765 A=0.000235
gnomAD - Exomes European Sub 135394 G=0.999911 A=0.000089
gnomAD - Exomes Asian Sub 49010 G=0.99906 A=0.00094
gnomAD - Exomes American Sub 34584 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16256 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6138 G=0.9998 A=0.0002
gnomAD - Genomes Global Study-wide 140252 G=0.999914 A=0.000086
gnomAD - Genomes European Sub 75952 G=0.99993 A=0.00007
gnomAD - Genomes African Sub 42030 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13662 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=0.9984 A=0.0016
gnomAD - Genomes Other Sub 2152 G=0.9991 A=0.0009
ExAC Global Study-wide 121394 G=0.999786 A=0.000214
ExAC Europe Sub 73344 G=0.99993 A=0.00007
ExAC Asian Sub 25164 G=0.99917 A=0.00083
ExAC American Sub 11576 G=1.00000 A=0.00000
ExAC African Sub 10402 G=1.00000 A=0.00000
ExAC Other Sub 908 G=1.000 A=0.000
The PAGE Study Global Study-wide 78698 G=0.99858 A=0.00142
The PAGE Study AfricanAmerican Sub 32516 G=0.99994 A=0.00006
The PAGE Study Mexican Sub 10808 G=0.99991 A=0.00009
The PAGE Study Asian Sub 8316 G=0.9877 A=0.0123
The PAGE Study PuertoRican Sub 7918 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 G=0.9985 A=0.0015
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 45080 G=0.99991 A=0.00009
Allele Frequency Aggregator European Sub 32728 G=0.99994 A=0.00006
Allele Frequency Aggregator Other Sub 6972 G=0.9997 A=0.0003
Allele Frequency Aggregator African Sub 3946 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 202 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 104 G=1.000 A=0.000
14KJPN JAPANESE Study-wide 28258 G=0.98117 A=0.01883
8.3KJPN JAPANESE Study-wide 16760 G=0.98115 A=0.01885
1000Genomes_30x Global Study-wide 6404 G=0.9997 A=0.0003
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=0.9983 A=0.0017
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9998 A=0.0002
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9938 A=0.0062
Korean Genome Project KOREAN Study-wide 1832 G=0.9951 A=0.0049
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.85267844G>A
GRCh37.p13 chr 1 NC_000001.10:g.85733527G>A
BCL10 RefSeqGene (LRG_1210) NG_012216.2:g.14061C>T
Gene: BCL10, BCL10 immune signaling adaptor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
BCL10 transcript variant 1 NM_003921.5:c.485C>T T [ACG] > M [ATG] Coding Sequence Variant
B-cell lymphoma/leukemia 10 isoform 1 NP_003912.1:p.Thr162Met T (Thr) > M (Met) Missense Variant
BCL10 transcript variant 2 NM_001320715.2:c.452C>T T [ACG] > M [ATG] Coding Sequence Variant
B-cell lymphoma/leukemia 10 isoform 2 NP_001307644.1:p.Thr151Met T (Thr) > M (Met) Missense Variant
BCL10 transcript variant X1 XM_011542397.4:c.644C>T T [ACG] > M [ATG] Coding Sequence Variant
B-cell lymphoma/leukemia 10 isoform X1 XP_011540699.1:p.Thr215Met T (Thr) > M (Met) Missense Variant
BCL10 transcript variant X2 XM_011542398.3:c.611C>T T [ACG] > M [ATG] Coding Sequence Variant
B-cell lymphoma/leukemia 10 isoform X2 XP_011540700.1:p.Thr204Met T (Thr) > M (Met) Missense Variant
BCL10 transcript variant X3 XM_011542399.3:c.431C>T T [ACG] > M [ATG] Coding Sequence Variant
B-cell lymphoma/leukemia 10 isoform X3 XP_011540701.1:p.Thr144Met T (Thr) > M (Met) Missense 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 G= A
GRCh38.p14 chr 1 NC_000001.11:g.85267844= NC_000001.11:g.85267844G>A
GRCh37.p13 chr 1 NC_000001.10:g.85733527= NC_000001.10:g.85733527G>A
BCL10 RefSeqGene (LRG_1210) NG_012216.2:g.14061= NG_012216.2:g.14061C>T
BCL10 transcript variant 1 NM_003921.5:c.485= NM_003921.5:c.485C>T
BCL10 transcript variant 1 NM_003921.4:c.485= NM_003921.4:c.485C>T
BCL10 transcript variant 2 NM_001320715.2:c.452= NM_001320715.2:c.452C>T
BCL10 transcript variant 2 NM_001320715.1:c.452= NM_001320715.1:c.452C>T
BCL10 transcript variant X1 XM_011542397.4:c.644= XM_011542397.4:c.644C>T
BCL10 transcript variant X1 XM_011542397.3:c.644= XM_011542397.3:c.644C>T
BCL10 transcript variant X1 XM_011542397.2:c.644= XM_011542397.2:c.644C>T
BCL10 transcript variant X1 XM_011542397.1:c.644= XM_011542397.1:c.644C>T
BCL10 transcript variant X3 XM_011542399.3:c.431= XM_011542399.3:c.431C>T
BCL10 transcript variant X3 XM_011542399.2:c.431= XM_011542399.2:c.431C>T
BCL10 transcript variant X4 XM_011542399.1:c.431= XM_011542399.1:c.431C>T
BCL10 transcript variant X2 XM_011542398.3:c.611= XM_011542398.3:c.611C>T
BCL10 transcript variant X2 XM_011542398.2:c.611= XM_011542398.2:c.611C>T
BCL10 transcript variant X2 XM_011542398.1:c.611= XM_011542398.1:c.611C>T
B-cell lymphoma/leukemia 10 isoform 1 NP_003912.1:p.Thr162= NP_003912.1:p.Thr162Met
B-cell lymphoma/leukemia 10 isoform 2 NP_001307644.1:p.Thr151= NP_001307644.1:p.Thr151Met
B-cell lymphoma/leukemia 10 isoform X1 XP_011540699.1:p.Thr215= XP_011540699.1:p.Thr215Met
B-cell lymphoma/leukemia 10 isoform X3 XP_011540701.1:p.Thr144= XP_011540701.1:p.Thr144Met
B-cell lymphoma/leukemia 10 isoform X2 XP_011540700.1:p.Thr204= XP_011540700.1:p.Thr204Met
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#.

30 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss488672756 May 04, 2012 (137)
2 1000GENOMES ss1291725941 Aug 21, 2014 (142)
3 BGI ss1558272120 Apr 01, 2015 (144)
4 EVA_EXAC ss1685619060 Apr 01, 2015 (144)
5 ILLUMINA ss1958289491 Feb 12, 2016 (147)
6 HUMAN_LONGEVITY ss2164232509 Dec 20, 2016 (150)
7 SYSTEMSBIOZJU ss2624417555 Nov 08, 2017 (151)
8 GNOMAD ss2731608675 Nov 08, 2017 (151)
9 GNOMAD ss2746364372 Nov 08, 2017 (151)
10 GNOMAD ss2757527675 Nov 08, 2017 (151)
11 ILLUMINA ss3021105737 Nov 08, 2017 (151)
12 ILLUMINA ss3651434241 Oct 11, 2018 (152)
13 ILLUMINA ss3725040960 Jul 12, 2019 (153)
14 EVA ss3746457534 Jul 12, 2019 (153)
15 PAGE_CC ss3770822244 Jul 12, 2019 (153)
16 KRGDB ss3894334882 Apr 25, 2020 (154)
17 KOGIC ss3944908708 Apr 25, 2020 (154)
18 TOPMED ss4457208949 Apr 25, 2021 (155)
19 TOMMO_GENOMICS ss5144876671 Apr 25, 2021 (155)
20 EVA ss5237269199 Apr 25, 2021 (155)
21 1000G_HIGH_COVERAGE ss5242990568 Oct 12, 2022 (156)
22 TRAN_CS_UWATERLOO ss5314396170 Oct 12, 2022 (156)
23 EVA ss5320062747 Oct 12, 2022 (156)
24 HUGCELL_USP ss5443978581 Oct 12, 2022 (156)
25 1000G_HIGH_COVERAGE ss5515657971 Oct 12, 2022 (156)
26 TOMMO_GENOMICS ss5669911963 Oct 12, 2022 (156)
27 EVA ss5847545335 Oct 12, 2022 (156)
28 EVA ss5909091377 Oct 12, 2022 (156)
29 EVA ss5935518507 Oct 12, 2022 (156)
30 EVA ss5979280532 Oct 12, 2022 (156)
31 1000Genomes NC_000001.10 - 85733527 Oct 11, 2018 (152)
32 1000Genomes_30x NC_000001.11 - 85267844 Oct 12, 2022 (156)
33 ExAC NC_000001.10 - 85733527 Oct 11, 2018 (152)
34 gnomAD - Genomes NC_000001.11 - 85267844 Apr 25, 2021 (155)
35 gnomAD - Exomes NC_000001.10 - 85733527 Jul 12, 2019 (153)
36 KOREAN population from KRGDB NC_000001.10 - 85733527 Apr 25, 2020 (154)
37 Korean Genome Project NC_000001.11 - 85267844 Apr 25, 2020 (154)
38 The PAGE Study NC_000001.11 - 85267844 Jul 12, 2019 (153)
39 8.3KJPN NC_000001.10 - 85733527 Apr 25, 2021 (155)
40 14KJPN NC_000001.11 - 85267844 Oct 12, 2022 (156)
41 TopMed NC_000001.11 - 85267844 Apr 25, 2021 (155)
42 ALFA NC_000001.11 - 85267844 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
ss1558272120 NC_000001.9:85506114:G:A NC_000001.11:85267843:G:A (self)
2475324, 4822102, 628881, 1512276, 2845978, ss488672756, ss1291725941, ss1685619060, ss1958289491, ss2624417555, ss2731608675, ss2746364372, ss2757527675, ss3021105737, ss3651434241, ss3746457534, ss3894334882, ss5144876671, ss5237269199, ss5320062747, ss5847545335, ss5935518507, ss5979280532 NC_000001.10:85733526:G:A NC_000001.11:85267843:G:A (self)
3183906, 17469025, 1286709, 43713, 3749067, 20815284, 6126127022, ss2164232509, ss3725040960, ss3770822244, ss3944908708, ss4457208949, ss5242990568, ss5314396170, ss5443978581, ss5515657971, ss5669911963, ss5909091377 NC_000001.11:85267843:G:A NC_000001.11:85267843:G:A (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 rs200837308

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