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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.

rs35489000

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:10286356 (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=0.004681 (1239/264690, TOPMED)
C=0.000908 (228/251098, GnomAD_exome)
C=0.000519 (119/229466, ALFA) (+ 8 more)
C=0.004877 (684/140246, GnomAD)
C=0.001211 (146/120528, ExAC)
C=0.00661 (520/78696, PAGE_STUDY)
C=0.00469 (61/13006, GO-ESP)
C=0.0047 (30/6404, 1000G_30x)
C=0.0036 (18/5008, 1000G)
T=0.5 (2/4, SGDP_PRJ)
C=0.5 (2/4, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CMBL : Missense Variant
Publications
1 citation
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 245816 T=0.999243 C=0.000757
European Sub 203848 T=0.999975 C=0.000025
African Sub 12004 T=0.98742 C=0.01258
African Others Sub 434 T=0.979 C=0.021
African American Sub 11570 T=0.98773 C=0.01227
Asian Sub 6690 T=1.0000 C=0.0000
East Asian Sub 4802 T=1.0000 C=0.0000
Other Asian Sub 1888 T=1.0000 C=0.0000
Latin American 1 Sub 1186 T=0.9924 C=0.0076
Latin American 2 Sub 1284 T=0.9992 C=0.0008
South Asian Sub 360 T=1.000 C=0.000
Other Sub 20444 T=0.99902 C=0.00098


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=0.995319 C=0.004681
gnomAD - Exomes Global Study-wide 251098 T=0.999092 C=0.000908
gnomAD - Exomes European Sub 135224 T=0.999985 C=0.000015
gnomAD - Exomes Asian Sub 48934 T=1.00000 C=0.00000
gnomAD - Exomes American Sub 34508 T=0.99983 C=0.00017
gnomAD - Exomes African Sub 16254 T=0.98646 C=0.01354
gnomAD - Exomes Ashkenazi Jewish Sub 10060 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6118 T=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 229466 T=0.999481 C=0.000519
Allele Frequency Aggregator European Sub 193766 T=0.999974 C=0.000026
Allele Frequency Aggregator Other Sub 19012 T=0.99921 C=0.00079
Allele Frequency Aggregator African Sub 7168 T=0.9876 C=0.0124
Allele Frequency Aggregator Asian Sub 6690 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 1284 T=0.9992 C=0.0008
Allele Frequency Aggregator Latin American 1 Sub 1186 T=0.9924 C=0.0076
Allele Frequency Aggregator South Asian Sub 360 T=1.000 C=0.000
gnomAD - Genomes Global Study-wide 140246 T=0.995123 C=0.004877
gnomAD - Genomes European Sub 75942 T=0.99999 C=0.00001
gnomAD - Genomes African Sub 42048 T=0.98399 C=0.01601
gnomAD - Genomes American Sub 13656 T=0.99949 C=0.00051
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3124 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2154 T=0.9986 C=0.0014
ExAC Global Study-wide 120528 T=0.998789 C=0.001211
ExAC Europe Sub 73090 T=1.00000 C=0.00000
ExAC Asian Sub 24566 T=1.00000 C=0.00000
ExAC American Sub 11572 T=1.00000 C=0.00000
ExAC African Sub 10400 T=0.98596 C=0.01404
ExAC Other Sub 900 T=1.000 C=0.000
The PAGE Study Global Study-wide 78696 T=0.99339 C=0.00661
The PAGE Study AfricanAmerican Sub 32516 T=0.98542 C=0.01458
The PAGE Study Mexican Sub 10808 T=0.99981 C=0.00019
The PAGE Study Asian Sub 8318 T=1.0000 C=0.0000
The PAGE Study PuertoRican Sub 7916 T=0.9985 C=0.0015
The PAGE Study NativeHawaiian Sub 4534 T=0.9998 C=0.0002
The PAGE Study Cuban Sub 4230 T=0.9981 C=0.0019
The PAGE Study Dominican Sub 3828 T=0.9953 C=0.0047
The PAGE Study CentralAmerican Sub 2450 T=0.9992 C=0.0008
The PAGE Study SouthAmerican Sub 1982 T=0.9990 C=0.0010
The PAGE Study NativeAmerican Sub 1260 T=0.9992 C=0.0008
The PAGE Study SouthAsian Sub 854 T=1.000 C=0.000
GO Exome Sequencing Project Global Study-wide 13006 T=0.99531 C=0.00469
GO Exome Sequencing Project European American Sub 8600 T=1.0000 C=0.0000
GO Exome Sequencing Project African American Sub 4406 T=0.9862 C=0.0138
1000Genomes_30x Global Study-wide 6404 T=0.9953 C=0.0047
1000Genomes_30x African Sub 1786 T=0.9832 C=0.0168
1000Genomes_30x Europe Sub 1266 T=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 T=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=1.000 C=0.000
1000Genomes Global Study-wide 5008 T=0.9964 C=0.0036
1000Genomes African Sub 1322 T=0.9864 C=0.0136
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=1.000 C=0.000
SGDP_PRJ Global Study-wide 4 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 5 NC_000005.10:g.10286356T>C
GRCh37.p13 chr 5 NC_000005.9:g.10286468T>C
Gene: CMBL, carboxymethylenebutenolidase homolog (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CMBL transcript NM_138809.4:c.464A>G Y [TAT] > C [TGT] Coding Sequence Variant
carboxymethylenebutenolidase homolog NP_620164.1:p.Tyr155Cys Y (Tyr) > C (Cys) Missense Variant
CMBL transcript variant X1 XM_047416714.1:c.464A>G Y [TAT] > C [TGT] Coding Sequence Variant
carboxymethylenebutenolidase homolog isoform X1 XP_047272670.1:p.Tyr155Cys Y (Tyr) > C (Cys) Missense Variant
CMBL transcript variant X2 XM_047416715.1:c.464A>G Y [TAT] > C [TGT] Coding Sequence Variant
carboxymethylenebutenolidase homolog isoform X1 XP_047272671.1:p.Tyr155Cys Y (Tyr) > C (Cys) Missense Variant
CMBL transcript variant X3 XM_047416716.1:c.464A>G Y [TAT] > C [TGT] Coding Sequence Variant
carboxymethylenebutenolidase homolog isoform X1 XP_047272672.1:p.Tyr155Cys Y (Tyr) > C (Cys) Missense Variant
CMBL transcript variant X4 XM_047416717.1:c.464A>G Y [TAT] > C [TGT] Coding Sequence Variant
carboxymethylenebutenolidase homolog isoform X1 XP_047272673.1:p.Tyr155Cys Y (Tyr) > C (Cys) Missense Variant
CMBL transcript variant X5 XM_047416718.1:c.464A>G Y [TAT] > C [TGT] Coding Sequence Variant
carboxymethylenebutenolidase homolog isoform X1 XP_047272674.1:p.Tyr155Cys Y (Tyr) > C (Cys) 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 T= C
GRCh38.p14 chr 5 NC_000005.10:g.10286356= NC_000005.10:g.10286356T>C
GRCh37.p13 chr 5 NC_000005.9:g.10286468= NC_000005.9:g.10286468T>C
CMBL transcript NM_138809.4:c.464= NM_138809.4:c.464A>G
CMBL transcript NM_138809.3:c.464= NM_138809.3:c.464A>G
CMBL transcript variant X1 XM_047416714.1:c.464= XM_047416714.1:c.464A>G
CMBL transcript variant X5 XM_047416718.1:c.464= XM_047416718.1:c.464A>G
CMBL transcript variant X4 XM_047416717.1:c.464= XM_047416717.1:c.464A>G
CMBL transcript variant X2 XM_047416715.1:c.464= XM_047416715.1:c.464A>G
CMBL transcript variant X3 XM_047416716.1:c.464= XM_047416716.1:c.464A>G
carboxymethylenebutenolidase homolog NP_620164.1:p.Tyr155= NP_620164.1:p.Tyr155Cys
carboxymethylenebutenolidase homolog isoform X1 XP_047272670.1:p.Tyr155= XP_047272670.1:p.Tyr155Cys
carboxymethylenebutenolidase homolog isoform X1 XP_047272674.1:p.Tyr155= XP_047272674.1:p.Tyr155Cys
carboxymethylenebutenolidase homolog isoform X1 XP_047272673.1:p.Tyr155= XP_047272673.1:p.Tyr155Cys
carboxymethylenebutenolidase homolog isoform X1 XP_047272671.1:p.Tyr155= XP_047272671.1:p.Tyr155Cys
carboxymethylenebutenolidase homolog isoform X1 XP_047272672.1:p.Tyr155= XP_047272672.1:p.Tyr155Cys
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#.

55 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss48411524 Mar 15, 2006 (126)
2 PERLEGEN ss68927180 May 18, 2007 (127)
3 ILLUMINA ss160627320 Dec 01, 2009 (131)
4 1000GENOMES ss221515340 Jul 14, 2010 (132)
5 NHLBI-ESP ss342177832 May 09, 2011 (134)
6 ILLUMINA ss481724036 Sep 08, 2015 (146)
7 ILLUMINA ss482578960 May 04, 2012 (137)
8 ILLUMINA ss484896760 May 04, 2012 (137)
9 1000GENOMES ss490900303 May 04, 2012 (137)
10 EXOME_CHIP ss491364470 May 04, 2012 (137)
11 ILLUMINA ss534710276 Sep 08, 2015 (146)
12 ILLUMINA ss780029984 Sep 08, 2015 (146)
13 ILLUMINA ss781808085 Sep 08, 2015 (146)
14 ILLUMINA ss835510144 Sep 08, 2015 (146)
15 1000GENOMES ss1313890316 Aug 21, 2014 (142)
16 EVA_EXAC ss1687749337 Apr 01, 2015 (144)
17 ILLUMINA ss1752539826 Sep 08, 2015 (146)
18 ILLUMINA ss1917788017 Feb 12, 2016 (147)
19 ILLUMINA ss1946138340 Feb 12, 2016 (147)
20 ILLUMINA ss1958766585 Feb 12, 2016 (147)
21 HUMAN_LONGEVITY ss2271345539 Dec 20, 2016 (150)
22 ILLUMINA ss2634245809 Nov 08, 2017 (151)
23 GNOMAD ss2734906932 Nov 08, 2017 (151)
24 GNOMAD ss2747357379 Nov 08, 2017 (151)
25 GNOMAD ss2821106709 Nov 08, 2017 (151)
26 AFFY ss2985315643 Nov 08, 2017 (151)
27 ILLUMINA ss3022465897 Nov 08, 2017 (151)
28 ILLUMINA ss3629177477 Oct 12, 2018 (152)
29 ILLUMINA ss3632174622 Oct 12, 2018 (152)
30 ILLUMINA ss3634991163 Oct 12, 2018 (152)
31 ILLUMINA ss3636700588 Oct 12, 2018 (152)
32 ILLUMINA ss3640698456 Oct 12, 2018 (152)
33 ILLUMINA ss3642398609 Oct 12, 2018 (152)
34 ILLUMINA ss3644871224 Oct 12, 2018 (152)
35 ILLUMINA ss3652958752 Oct 12, 2018 (152)
36 ILLUMINA ss3654088411 Oct 12, 2018 (152)
37 ILLUMINA ss3726212916 Jul 13, 2019 (153)
38 ILLUMINA ss3744533390 Jul 13, 2019 (153)
39 ILLUMINA ss3745291289 Jul 13, 2019 (153)
40 PAGE_CC ss3771186507 Jul 13, 2019 (153)
41 ILLUMINA ss3772785660 Jul 13, 2019 (153)
42 KHV_HUMAN_GENOMES ss3806230062 Jul 13, 2019 (153)
43 EVA ss3824070033 Apr 26, 2020 (154)
44 SGDP_PRJ ss3861205816 Apr 26, 2020 (154)
45 EVA ss3986301991 Apr 26, 2021 (155)
46 TOPMED ss4649469525 Apr 26, 2021 (155)
47 1000G_HIGH_COVERAGE ss5262864537 Oct 13, 2022 (156)
48 EVA ss5355631133 Oct 13, 2022 (156)
49 HUGCELL_USP ss5461212493 Oct 13, 2022 (156)
50 1000G_HIGH_COVERAGE ss5545907156 Oct 13, 2022 (156)
51 SANFORD_IMAGENETICS ss5637178228 Oct 13, 2022 (156)
52 EVA ss5848041341 Oct 13, 2022 (156)
53 EVA ss5892977735 Oct 13, 2022 (156)
54 EVA ss5965589625 Oct 13, 2022 (156)
55 EVA ss5979731422 Oct 13, 2022 (156)
56 1000Genomes NC_000005.9 - 10286468 Oct 12, 2018 (152)
57 1000Genomes_30x NC_000005.10 - 10286356 Oct 13, 2022 (156)
58 ExAC NC_000005.9 - 10286468 Oct 12, 2018 (152)
59 gnomAD - Genomes NC_000005.10 - 10286356 Apr 26, 2021 (155)
60 gnomAD - Exomes NC_000005.9 - 10286468 Jul 13, 2019 (153)
61 GO Exome Sequencing Project NC_000005.9 - 10286468 Oct 12, 2018 (152)
62 The PAGE Study NC_000005.10 - 10286356 Jul 13, 2019 (153)
63 SGDP_PRJ NC_000005.9 - 10286468 Apr 26, 2020 (154)
64 TopMed NC_000005.10 - 10286356 Apr 26, 2021 (155)
65 ALFA NC_000005.10 - 10286356 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss484896760 NC_000005.8:10339467:T:C NC_000005.10:10286355:T:C (self)
25444475, 7735339, 4022055, 528186, 13222796, ss221515340, ss342177832, ss481724036, ss482578960, ss490900303, ss491364470, ss534710276, ss780029984, ss781808085, ss835510144, ss1313890316, ss1687749337, ss1752539826, ss1917788017, ss1946138340, ss1958766585, ss2634245809, ss2734906932, ss2747357379, ss2821106709, ss2985315643, ss3022465897, ss3629177477, ss3632174622, ss3634991163, ss3636700588, ss3640698456, ss3642398609, ss3644871224, ss3652958752, ss3654088411, ss3744533390, ss3745291289, ss3772785660, ss3824070033, ss3861205816, ss3986301991, ss5355631133, ss5637178228, ss5848041341, ss5965589625, ss5979731422 NC_000005.9:10286467:T:C NC_000005.10:10286355:T:C (self)
33433091, 179805052, 407976, 486847082, 1313168763, ss2271345539, ss3726212916, ss3771186507, ss3806230062, ss4649469525, ss5262864537, ss5461212493, ss5545907156, ss5892977735 NC_000005.10:10286355:T:C NC_000005.10:10286355:T:C (self)
ss48411524, ss68927180, ss160627320 NT_006576.16:10276467:T:C NC_000005.10:10286355: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.

1 citation for rs35489000
PMID Title Author Year Journal
23471504 Interindividual variability of carboxymethylenebutenolidase homolog, a novel olmesartan medoxomil hydrolase, in the human liver and intestine. Ishizuka T et al. 2013 Drug metabolism and disposition
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