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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 Aliases 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.

rs12716981

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr16:31106703 (GRCh38.p12) 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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.38994 (48964/125568, TOPMED)
A=0.3761 (11788/31344, GnomAD)
A=0.420 (2104/5008, 1000G) (+ 5 more)
A=0.344 (1542/4480, Estonian)
A=0.364 (1402/3854, ALSPAC)
A=0.361 (1340/3708, TWINSUK)
A=0.37 (223/600, NorthernSweden)
C=0.17 (37/212, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BCKDK : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 16 NC_000016.10:g.31106703C>A
GRCh37.p13 chr 16 NC_000016.9:g.31118024C>A
BCKDK RefSeqGene NG_033011.1:g.3410C>A
Gene: BCKDK, branched chain keto acid dehydrogenase kinase (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
BCKDK transcript variant 2 NM_001122957.3:c. N/A Upstream Transcript Variant
BCKDK transcript variant 3 NM_001271926.2:c. N/A Upstream Transcript Variant
BCKDK transcript variant 1 NM_005881.4:c. N/A Upstream Transcript Variant
BCKDK transcript variant X1 XM_017022859.1:c. N/A Upstream Transcript 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

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 125568 C=0.61006 A=0.38994
gnomAD - Genomes Global Study-wide 31344 C=0.6239 A=0.3761
gnomAD - Genomes European Sub 18864 C=0.6334 A=0.3666
gnomAD - Genomes African Sub 8696 C=0.707 A=0.293
gnomAD - Genomes East Asian Sub 1558 C=0.101 A=0.899
gnomAD - Genomes Other Sub 1088 C=0.630 A=0.370
gnomAD - Genomes American Sub 848 C=0.55 A=0.45
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.52 A=0.48
1000Genomes Global Study-wide 5008 C=0.580 A=0.420
1000Genomes African Sub 1322 C=0.707 A=0.293
1000Genomes East Asian Sub 1008 C=0.115 A=0.885
1000Genomes Europe Sub 1006 C=0.606 A=0.394
1000Genomes South Asian Sub 978 C=0.85 A=0.15
1000Genomes American Sub 694 C=0.59 A=0.41
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.656 A=0.344
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.636 A=0.364
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.639 A=0.361
Northern Sweden ACPOP Study-wide 600 C=0.63 A=0.37
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.17 A=0.83
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= A Note
GRCh38.p12 chr 16 NC_000016.10:g.31106703= NC_000016.10:g.31106703C>A
GRCh37.p13 chr 16 NC_000016.9:g.31118024= NC_000016.9:g.31118024C>A
BCKDK RefSeqGene NG_033011.1:g.3410= NG_033011.1:g.3410C>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#.

50 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss21342027 Apr 05, 2004 (121)
2 BCM_SSAHASNP ss22999359 Apr 05, 2004 (121)
3 HGSV ss78111490 Dec 06, 2007 (129)
4 BCMHGSC_JDW ss90365552 Mar 24, 2008 (129)
5 HUMANGENOME_JCVI ss96633893 Feb 05, 2009 (130)
6 BGI ss103290730 Dec 01, 2009 (131)
7 1000GENOMES ss109298644 Jan 23, 2009 (130)
8 ENSEMBL ss136659394 Dec 01, 2009 (131)
9 ENSEMBL ss136759861 Dec 01, 2009 (131)
10 GMI ss157248929 Dec 01, 2009 (131)
11 BUSHMAN ss201611329 Jul 04, 2010 (132)
12 BCM-HGSC-SUB ss207544865 Jul 04, 2010 (132)
13 1000GENOMES ss227214766 Jul 14, 2010 (132)
14 1000GENOMES ss237004909 Jul 15, 2010 (132)
15 1000GENOMES ss243348951 Jul 15, 2010 (132)
16 GMI ss282493671 May 04, 2012 (137)
17 GMI ss287058912 Apr 25, 2013 (138)
18 PJP ss291944773 May 09, 2011 (134)
19 TISHKOFF ss564870532 Apr 25, 2013 (138)
20 SSMP ss660625339 Apr 25, 2013 (138)
21 EVA-GONL ss992432633 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1080589047 Aug 21, 2014 (142)
23 1000GENOMES ss1355977589 Aug 21, 2014 (142)
24 DDI ss1427823829 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1577894852 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1634304905 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1677298938 Apr 01, 2015 (144)
28 EVA_DECODE ss1696467042 Apr 01, 2015 (144)
29 WEILL_CORNELL_DGM ss1935857546 Feb 12, 2016 (147)
30 GENOMED ss1968250989 Jul 19, 2016 (147)
31 JJLAB ss2028715743 Sep 14, 2016 (149)
32 USC_VALOUEV ss2157130015 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2211738774 Dec 20, 2016 (150)
34 TOPMED ss2376534889 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2628850416 Nov 08, 2017 (151)
36 GRF ss2701637593 Nov 08, 2017 (151)
37 GNOMAD ss2942120662 Nov 08, 2017 (151)
38 SWEGEN ss3014335376 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3028180758 Nov 08, 2017 (151)
40 TOPMED ss3244234959 Nov 08, 2017 (151)
41 CSHL ss3351408518 Nov 08, 2017 (151)
42 URBANLAB ss3650498592 Oct 12, 2018 (152)
43 EGCUT_WGS ss3681408975 Jul 13, 2019 (153)
44 EVA_DECODE ss3699138692 Jul 13, 2019 (153)
45 ACPOP ss3741465879 Jul 13, 2019 (153)
46 EVA ss3753863772 Jul 13, 2019 (153)
47 PACBIO ss3788022312 Jul 13, 2019 (153)
48 PACBIO ss3793008659 Jul 13, 2019 (153)
49 PACBIO ss3797893550 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3819156802 Jul 13, 2019 (153)
51 1000Genomes NC_000016.9 - 31118024 Oct 12, 2018 (152)
52 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 31118024 Oct 12, 2018 (152)
53 Genetic variation in the Estonian population NC_000016.9 - 31118024 Oct 12, 2018 (152)
54 gnomAD - Genomes NC_000016.9 - 31118024 Jul 13, 2019 (153)
55 Northern Sweden NC_000016.9 - 31118024 Jul 13, 2019 (153)
56 TopMed NC_000016.10 - 31106703 Oct 12, 2018 (152)
57 UK 10K study - Twins NC_000016.9 - 31118024 Oct 12, 2018 (152)
58 A Vietnamese Genetic Variation Database NC_000016.9 - 31118024 Jul 13, 2019 (153)
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
ss78111490, ss90365552, ss109298644, ss201611329, ss207544865, ss282493671, ss287058912, ss291944773, ss1696467042 NC_000016.8:31025524:C:A NC_000016.10:31106702:C:A (self)
69132578, 38370440, 27147223, 188666597, 14750744, 38370440, 8518790, ss227214766, ss237004909, ss243348951, ss564870532, ss660625339, ss992432633, ss1080589047, ss1355977589, ss1427823829, ss1577894852, ss1634304905, ss1677298938, ss1935857546, ss1968250989, ss2028715743, ss2157130015, ss2376534889, ss2628850416, ss2701637593, ss2942120662, ss3014335376, ss3351408518, ss3681408975, ss3741465879, ss3753863772, ss3788022312, ss3793008659, ss3797893550 NC_000016.9:31118023:C:A NC_000016.10:31106702:C:A (self)
142687004, ss2211738774, ss3028180758, ss3244234959, ss3650498592, ss3699138692, ss3819156802 NC_000016.10:31106702:C:A NC_000016.10:31106702:C:A (self)
ss96633893, ss103290730, ss136659394, ss136759861, ss157248929 NT_010393.16:31058023:C:A NC_000016.10:31106702:C:A (self)
ss21342027, ss22999359 NT_024812.10:2517690:C:A NC_000016.10:31106702:C: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 rs12716981

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.post308+0fe9b3b