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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.

rs2856586

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr16:16172741 (GRCh38.p13) 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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.394254 (104355/264690, TOPMED)
C=0.394681 (55234/139946, GnomAD)
C=0.40950 (8217/20066, ALFA) (+ 13 more)
C=0.49212 (8248/16760, 8.3KJPN)
C=0.4529 (2268/5008, 1000G)
C=0.4241 (1900/4480, Estonian)
C=0.4209 (1622/3854, ALSPAC)
C=0.4248 (1575/3708, TWINSUK)
C=0.4922 (1442/2930, KOREAN)
C=0.403 (402/998, GoNL)
C=0.387 (232/600, NorthernSweden)
G=0.338 (144/426, SGDP_PRJ)
G=0.440 (95/216, Qatari)
G=0.397 (85/214, Vietnamese)
G=0.38 (16/42, Siberian)
C=0.33 (13/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ABCC6 : Intron 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.p13 chr 16 NC_000016.10:g.16172741G>C
GRCh37.p13 chr 16 NC_000016.9:g.16266598G>C
ABCC6 RefSeqGene (LRG_1115) NG_007558.3:g.55877C>G
ABCC6 RefSeqGene NG_007558.2:g.55731C>G
GRCh38.p13 chr 16 alt locus HSCHR16_1_CTG1 NT_187607.1:g.1830752G>C
Gene: ABCC6, ATP binding cassette subfamily C member 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ABCC6 transcript variant 1 NM_001171.6:c.2787+543C>G N/A Intron Variant
ABCC6 transcript variant 3 NM_001351800.1:c.2445+543…

NM_001351800.1:c.2445+543C>G

N/A Intron Variant
ABCC6 transcript variant 2 NM_001079528.4:c. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant 4 NR_147784.1:n. N/A Intron Variant
ABCC6 transcript variant X1 XM_011522479.2:c.2754+543…

XM_011522479.2:c.2754+543C>G

N/A Intron Variant
ABCC6 transcript variant X4 XM_011522480.1:c.2445+543…

XM_011522480.1:c.2445+543C>G

N/A Intron Variant
ABCC6 transcript variant X5 XM_011522481.3:c.2445+543…

XM_011522481.3:c.2445+543C>G

N/A Intron Variant
ABCC6 transcript variant X2 XM_017023212.1:c.2619+543…

XM_017023212.1:c.2619+543C>G

N/A Intron Variant
ABCC6 transcript variant X8 XM_017023214.1:c.2787+543…

XM_017023214.1:c.2787+543C>G

N/A Intron Variant
ABCC6 transcript variant X10 XM_024450261.1:c.2823+543…

XM_024450261.1:c.2823+543C>G

N/A Intron Variant
ABCC6 transcript variant X9 XM_011522482.3:c. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant X3 XR_932836.2:n. N/A Intron Variant
ABCC6 transcript variant X6 XR_932837.3:n. N/A Intron Variant
ABCC6 transcript variant X7 XR_932838.3: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

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 20066 G=0.59050 C=0.40950
European Sub 15434 G=0.57140 C=0.42860
African Sub 2946 G=0.7077 C=0.2923
African Others Sub 114 G=0.746 C=0.254
African American Sub 2832 G=0.7062 C=0.2938
Asian Sub 112 G=0.500 C=0.500
East Asian Sub 86 G=0.52 C=0.48
Other Asian Sub 26 G=0.42 C=0.58
Latin American 1 Sub 146 G=0.603 C=0.397
Latin American 2 Sub 610 G=0.557 C=0.443
South Asian Sub 98 G=0.41 C=0.59
Other Sub 720 G=0.585 C=0.415


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=0.605746 C=0.394254
gnomAD - Genomes Global Study-wide 139946 G=0.605319 C=0.394681
gnomAD - Genomes European Sub 75838 G=0.57280 C=0.42720
gnomAD - Genomes African Sub 41894 G=0.68933 C=0.31067
gnomAD - Genomes American Sub 13628 G=0.59084 C=0.40916
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.5105 C=0.4895
gnomAD - Genomes East Asian Sub 3120 G=0.4401 C=0.5599
gnomAD - Genomes Other Sub 2146 G=0.5932 C=0.4068
8.3KJPN JAPANESE Study-wide 16760 G=0.50788 C=0.49212
1000Genomes Global Study-wide 5008 G=0.5471 C=0.4529
1000Genomes African Sub 1322 G=0.7080 C=0.2920
1000Genomes East Asian Sub 1008 G=0.4444 C=0.5556
1000Genomes Europe Sub 1006 G=0.5865 C=0.4135
1000Genomes South Asian Sub 978 G=0.333 C=0.667
1000Genomes American Sub 694 G=0.634 C=0.366
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.5759 C=0.4241
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.5791 C=0.4209
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.5752 C=0.4248
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.5078 C=0.4922
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.597 C=0.403
Northern Sweden ACPOP Study-wide 600 G=0.613 C=0.387
SGDP_PRJ Global Study-wide 426 G=0.338 C=0.662
Qatari Global Study-wide 216 G=0.440 C=0.560
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.397 C=0.603
Siberian Global Study-wide 42 G=0.38 C=0.62
The Danish reference pan genome Danish Study-wide 40 G=0.68 C=0.33
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= C
GRCh38.p13 chr 16 NC_000016.10:g.16172741= NC_000016.10:g.16172741G>C
GRCh37.p13 chr 16 NC_000016.9:g.16266598= NC_000016.9:g.16266598G>C
ABCC6 RefSeqGene (LRG_1115) NG_007558.3:g.55877= NG_007558.3:g.55877C>G
ABCC6 RefSeqGene NG_007558.2:g.55731= NG_007558.2:g.55731C>G
GRCh38.p13 chr 16 alt locus HSCHR16_1_CTG1 NT_187607.1:g.1830752= NT_187607.1:g.1830752G>C
ABCC6 transcript variant 1 NM_001171.5:c.2787+543= NM_001171.5:c.2787+543C>G
ABCC6 transcript variant 1 NM_001171.6:c.2787+543= NM_001171.6:c.2787+543C>G
ABCC6 transcript variant 3 NM_001351800.1:c.2445+543= NM_001351800.1:c.2445+543C>G
ABCC6 transcript variant X1 XM_011522479.2:c.2754+543= XM_011522479.2:c.2754+543C>G
ABCC6 transcript variant X4 XM_011522480.1:c.2445+543= XM_011522480.1:c.2445+543C>G
ABCC6 transcript variant X5 XM_011522481.3:c.2445+543= XM_011522481.3:c.2445+543C>G
ABCC6 transcript variant X2 XM_017023212.1:c.2619+543= XM_017023212.1:c.2619+543C>G
ABCC6 transcript variant X8 XM_017023214.1:c.2787+543= XM_017023214.1:c.2787+543C>G
ABCC6 transcript variant X10 XM_024450261.1:c.2823+543= XM_024450261.1:c.2823+543C>G
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#.

61 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4044140 Sep 28, 2001 (100)
2 BCMHGSC_JDW ss90334470 Mar 24, 2008 (129)
3 BGI ss103283202 Feb 23, 2009 (131)
4 1000GENOMES ss109235034 Jan 23, 2009 (130)
5 1000GENOMES ss114911343 Jan 25, 2009 (130)
6 ENSEMBL ss136614221 Dec 01, 2009 (131)
7 ILLUMINA ss152536314 Dec 01, 2009 (131)
8 ILLUMINA ss159102619 Dec 01, 2009 (131)
9 ILLUMINA ss159845997 Dec 01, 2009 (131)
10 ILLUMINA ss168870707 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss169309187 Jul 04, 2010 (132)
12 BUSHMAN ss201504154 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss207490504 Jul 04, 2010 (132)
14 1000GENOMES ss227170997 Jul 14, 2010 (132)
15 1000GENOMES ss236973348 Jul 15, 2010 (132)
16 1000GENOMES ss243323880 Jul 15, 2010 (132)
17 BL ss255552389 May 09, 2011 (134)
18 GMI ss282457600 May 04, 2012 (137)
19 ILLUMINA ss479154422 Mar 15, 2016 (147)
20 ILLUMINA ss532727810 Mar 15, 2016 (147)
21 SSMP ss660562078 Apr 25, 2013 (138)
22 ILLUMINA ss832615415 Mar 15, 2016 (147)
23 ILLUMINA ss833206104 Mar 15, 2016 (147)
24 EVA-GONL ss992338157 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1080526062 Aug 21, 2014 (142)
26 1000GENOMES ss1355598420 Aug 21, 2014 (142)
27 DDI ss1427794633 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1577858043 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1634121896 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1677115929 Apr 01, 2015 (144)
31 EVA_DECODE ss1696373356 Apr 01, 2015 (144)
32 HAMMER_LAB ss1808446509 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1935755710 Feb 12, 2016 (147)
34 GENOMED ss1968232364 Jul 19, 2016 (147)
35 JJLAB ss2028664829 Sep 14, 2016 (149)
36 USC_VALOUEV ss2157076378 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2211038198 Dec 20, 2016 (150)
38 TOPMED ss2375727244 Dec 20, 2016 (150)
39 SYSTEMSBIOZJU ss2628826567 Nov 08, 2017 (151)
40 GRF ss2701575357 Nov 08, 2017 (151)
41 GNOMAD ss2940929345 Nov 08, 2017 (151)
42 SWEGEN ss3014156971 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3028158014 Nov 08, 2017 (151)
44 TOPMED ss3241493492 Nov 08, 2017 (151)
45 CSHL ss3351363009 Nov 08, 2017 (151)
46 EGCUT_WGS ss3681270083 Jul 13, 2019 (153)
47 EVA_DECODE ss3698945588 Jul 13, 2019 (153)
48 ACPOP ss3741382420 Jul 13, 2019 (153)
49 EVA ss3753751577 Jul 13, 2019 (153)
50 PACBIO ss3787995636 Jul 13, 2019 (153)
51 PACBIO ss3792986712 Jul 13, 2019 (153)
52 PACBIO ss3797871682 Jul 13, 2019 (153)
53 KHV_HUMAN_GENOMES ss3819045415 Jul 13, 2019 (153)
54 EVA ss3834501536 Apr 27, 2020 (154)
55 EVA ss3840856286 Apr 27, 2020 (154)
56 EVA ss3846347664 Apr 27, 2020 (154)
57 SGDP_PRJ ss3884058187 Apr 27, 2020 (154)
58 KRGDB ss3933369880 Apr 27, 2020 (154)
59 VINODS ss4032512718 Apr 27, 2021 (155)
60 TOPMED ss5009589163 Apr 27, 2021 (155)
61 TOMMO_GENOMICS ss5218677285 Apr 27, 2021 (155)
62 1000Genomes NC_000016.9 - 16266598 Oct 12, 2018 (152)
63 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 16266598 Oct 12, 2018 (152)
64 Genetic variation in the Estonian population NC_000016.9 - 16266598 Oct 12, 2018 (152)
65 The Danish reference pan genome NC_000016.9 - 16266598 Apr 27, 2020 (154)
66 gnomAD - Genomes NC_000016.10 - 16172741 Apr 27, 2021 (155)
67 Genome of the Netherlands Release 5 NC_000016.9 - 16266598 Apr 27, 2020 (154)
68 KOREAN population from KRGDB NC_000016.9 - 16266598 Apr 27, 2020 (154)
69 Northern Sweden NC_000016.9 - 16266598 Jul 13, 2019 (153)
70 Qatari NC_000016.9 - 16266598 Apr 27, 2020 (154)
71 SGDP_PRJ NC_000016.9 - 16266598 Apr 27, 2020 (154)
72 Siberian NC_000016.9 - 16266598 Apr 27, 2020 (154)
73 8.3KJPN NC_000016.9 - 16266598 Apr 27, 2021 (155)
74 TopMed NC_000016.10 - 16172741 Apr 27, 2021 (155)
75 UK 10K study - Twins NC_000016.9 - 16266598 Oct 12, 2018 (152)
76 A Vietnamese Genetic Variation Database NC_000016.9 - 16266598 Jul 13, 2019 (153)
77 ALFA NC_000016.10 - 16172741 Apr 27, 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)
rs74246637 Dec 02, 2009 (131)
rs386419939 Jul 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss90334470, ss109235034, ss114911343, ss159845997, ss169309187, ss201504154, ss207490504, ss255552389, ss282457600, ss1696373356 NC_000016.8:16174098:G:C NC_000016.10:16172740:G:C (self)
68740141, 38166831, 27008331, 4072745, 17025189, 40547274, 14667285, 17797632, 36075167, 9592732, 76646592, 38166831, 8478585, ss227170997, ss236973348, ss243323880, ss660562078, ss992338157, ss1080526062, ss1355598420, ss1427794633, ss1577858043, ss1634121896, ss1677115929, ss1808446509, ss1935755710, ss1968232364, ss2028664829, ss2157076378, ss2375727244, ss2628826567, ss2701575357, ss2940929345, ss3014156971, ss3351363009, ss3681270083, ss3741382420, ss3753751577, ss3787995636, ss3792986712, ss3797871682, ss3834501536, ss3840856286, ss3884058187, ss3933369880, ss5218677285 NC_000016.9:16266597:G:C NC_000016.10:16172740:G:C (self)
484394639, 140707517, 225134824, 10652085649, ss2211038198, ss3028158014, ss3241493492, ss3698945588, ss3819045415, ss3846347664, ss5009589163 NC_000016.10:16172740:G:C NC_000016.10:16172740:G:C (self)
ss4044140, ss103283202, ss136614221, ss152536314, ss159102619, ss168870707, ss479154422, ss532727810, ss832615415, ss833206104 NT_010393.16:16206597:G:C NC_000016.10:16172740:G:C (self)
ss4032512718 NT_187607.1:1830751:G:C NC_000016.10:16172740:G:C
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 rs2856586

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.post596+ae089ad