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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.

rs72657689

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:16169793 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000382 (101/264690, TOPMED)
T=0.000551 (104/188620, GnomAD_exome)
T=0.000721 (134/185924, ALFA) (+ 6 more)
T=0.000371 (52/140270, GnomAD)
T=0.00006 (5/78694, PAGE_STUDY)
T=0.00068 (26/37964, ExAC)
T=0.00004 (1/28258, 14KJPN)
T=0.00006 (1/16760, 8.3KJPN)
T=0.00039 (5/12946, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ABCC6 : 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 202336 C=0.999323 T=0.000677
European Sub 171874 C=0.999343 T=0.000657
African Sub 9710 C=0.9998 T=0.0002
African Others Sub 354 C=1.000 T=0.000
African American Sub 9356 C=0.9998 T=0.0002
Asian Sub 3390 C=1.0000 T=0.0000
East Asian Sub 2710 C=1.0000 T=0.0000
Other Asian Sub 680 C=1.000 T=0.000
Latin American 1 Sub 796 C=1.000 T=0.000
Latin American 2 Sub 968 C=1.000 T=0.000
South Asian Sub 276 C=1.000 T=0.000
Other Sub 15322 C=0.99856 T=0.00144


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 C=0.999618 T=0.000382
gnomAD - Exomes Global Study-wide 188620 C=0.999449 T=0.000551
gnomAD - Exomes European Sub 96832 C=0.99989 T=0.00011
gnomAD - Exomes Asian Sub 39096 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 27594 C=0.99989 T=0.00011
gnomAD - Exomes African Sub 11222 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 8878 C=0.9904 T=0.0096
gnomAD - Exomes Other Sub 4998 C=0.9990 T=0.0010
Allele Frequency Aggregator Total Global 185924 C=0.999279 T=0.000721
Allele Frequency Aggregator European Sub 161734 C=0.999320 T=0.000680
Allele Frequency Aggregator Other Sub 13888 C=0.99842 T=0.00158
Allele Frequency Aggregator African Sub 4872 C=0.9996 T=0.0004
Allele Frequency Aggregator Asian Sub 3390 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 968 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 796 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 276 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 140270 C=0.999629 T=0.000371
gnomAD - Genomes European Sub 75954 C=0.99989 T=0.00011
gnomAD - Genomes African Sub 42044 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13664 C=0.99993 T=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9877 T=0.0123
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=0.9991 T=0.0009
The PAGE Study Global Study-wide 78694 C=0.99994 T=0.00006
The PAGE Study AfricanAmerican Sub 32510 C=1.00000 T=0.00000
The PAGE Study Mexican Sub 10810 C=1.00000 T=0.00000
The PAGE Study Asian Sub 8316 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=0.9998 T=0.0002
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=0.9985 T=0.0015
The PAGE Study NativeAmerican Sub 1260 C=0.9992 T=0.0008
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
ExAC Global Study-wide 37964 C=0.99932 T=0.00068
ExAC Europe Sub 20180 C=0.99871 T=0.00129
ExAC Asian Sub 11538 C=1.00000 T=0.00000
ExAC African Sub 3970 C=1.0000 T=0.0000
ExAC American Sub 1966 C=1.0000 T=0.0000
ExAC Other Sub 310 C=1.000 T=0.000
14KJPN JAPANESE Study-wide 28258 C=0.99996 T=0.00004
8.3KJPN JAPANESE Study-wide 16760 C=0.99994 T=0.00006
GO Exome Sequencing Project Global Study-wide 12946 C=0.99961 T=0.00039
GO Exome Sequencing Project European American Sub 8582 C=0.9994 T=0.0006
GO Exome Sequencing Project African American Sub 4364 C=1.0000 T=0.0000
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 16 NC_000016.10:g.16169793C>T
GRCh37.p13 chr 16 NC_000016.9:g.16263650C>T
ABCC6 RefSeqGene (LRG_1115) NG_007558.3:g.58825G>A
GRCh38.p14 chr 16 alt locus HSCHR16_1_CTG1 NT_187607.1:g.1827899C>T
Gene: ABCC6, ATP binding cassette subfamily C member 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ABCC6 transcript variant 2 NM_001079528.4:c. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant 3 NM_001351800.1:c.2506G>A A [GCA] > T [ACA] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform 3 NP_001338729.1:p.Ala836Thr A (Ala) > T (Thr) Missense Variant
ABCC6 transcript variant 1 NM_001171.6:c.2848G>A A [GCA] > T [ACA] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform 1 NP_001162.5:p.Ala950Thr A (Ala) > T (Thr) Missense Variant
ABCC6 transcript variant 4 NR_147784.1:n.2710G>A N/A Non Coding Transcript Variant
ABCC6 transcript variant X10 XM_011522482.4:c. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant X3 XM_011522480.1:c.2506G>A A [GCA] > T [ACA] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform X3 XP_011520782.1:p.Ala836Thr A (Ala) > T (Thr) Missense Variant
ABCC6 transcript variant X1 XM_011522479.3:c.2815G>A A [GCA] > T [ACA] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform X1 XP_011520781.1:p.Ala939Thr A (Ala) > T (Thr) Missense Variant
ABCC6 transcript variant X2 XM_017023212.2:c.2680G>A A [GCA] > T [ACA] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform X2 XP_016878701.1:p.Ala894Thr A (Ala) > T (Thr) Missense Variant
ABCC6 transcript variant X4 XM_011522481.4:c.2506G>A A [GCA] > T [ACA] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform X3 XP_011520783.1:p.Ala836Thr A (Ala) > T (Thr) Missense Variant
ABCC6 transcript variant X8 XM_017023214.2:c.2848G>A A [GCA] > T [ACA] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform X4 XP_016878703.1:p.Ala950Thr A (Ala) > T (Thr) Missense Variant
ABCC6 transcript variant X9 XM_047434069.1:c.2680G>A A [GCA] > T [ACA] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform X5 XP_047290025.1:p.Ala894Thr A (Ala) > T (Thr) Missense Variant
ABCC6 transcript variant X5 XR_932836.3:n.2908G>A N/A Non Coding Transcript Variant
ABCC6 transcript variant X6 XR_932838.4:n.2908G>A N/A Non Coding Transcript Variant
ABCC6 transcript variant X7 XR_932837.4:n.2908G>A N/A Non Coding 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.

Allele: T (allele ID: 375082 )
ClinVar Accession Disease Names Clinical Significance
RCV000437137.5 not provided Benign-Likely-Benign
RCV000499095.4 Pseudoxanthoma elasticum Benign
RCV002253430.1 Pseudoxanthoma elasticum, forme fruste Benign
RCV002253431.1 Arterial calcification, generalized, of infancy, 2 Benign
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= T
GRCh38.p14 chr 16 NC_000016.10:g.16169793= NC_000016.10:g.16169793C>T
GRCh37.p13 chr 16 NC_000016.9:g.16263650= NC_000016.9:g.16263650C>T
ABCC6 RefSeqGene (LRG_1115) NG_007558.3:g.58825= NG_007558.3:g.58825G>A
ABCC6 transcript variant 1 NM_001171.6:c.2848= NM_001171.6:c.2848G>A
ABCC6 transcript variant 1 NM_001171.5:c.2848= NM_001171.5:c.2848G>A
ABCC6 transcript variant 3 NM_001351800.1:c.2506= NM_001351800.1:c.2506G>A
ABCC6 transcript variant 4 NR_147784.1:n.2710= NR_147784.1:n.2710G>A
GRCh38.p14 chr 16 alt locus HSCHR16_1_CTG1 NT_187607.1:g.1827899= NT_187607.1:g.1827899C>T
ABCC6 transcript variant X4 XM_011522481.4:c.2506= XM_011522481.4:c.2506G>A
ABCC6 transcript variant X5 XM_011522481.3:c.2506= XM_011522481.3:c.2506G>A
ABCC6 transcript variant X6 XM_011522481.2:c.2506= XM_011522481.2:c.2506G>A
ABCC6 transcript variant X3 XM_011522481.1:c.2506= XM_011522481.1:c.2506G>A
ABCC6 transcript variant X6 XR_932838.4:n.2908= XR_932838.4:n.2908G>A
ABCC6 transcript variant X7 XR_932838.3:n.3029= XR_932838.3:n.3029G>A
ABCC6 transcript variant X8 XR_932838.2:n.3029= XR_932838.2:n.3029G>A
ABCC6 transcript variant X5 XR_932838.1:n.3084= XR_932838.1:n.3084G>A
ABCC6 transcript variant X7 XR_932837.4:n.2908= XR_932837.4:n.2908G>A
ABCC6 transcript variant X6 XR_932837.3:n.3029= XR_932837.3:n.3029G>A
ABCC6 transcript variant X7 XR_932837.2:n.3028= XR_932837.2:n.3028G>A
ABCC6 transcript variant X4 XR_932837.1:n.3084= XR_932837.1:n.3084G>A
ABCC6 transcript variant X5 XR_932836.3:n.2908= XR_932836.3:n.2908G>A
ABCC6 transcript variant X3 XR_932836.2:n.3029= XR_932836.2:n.3029G>A
ABCC6 transcript variant X1 XR_932836.1:n.3083= XR_932836.1:n.3083G>A
ABCC6 transcript variant X2 XM_017023212.2:c.2680= XM_017023212.2:c.2680G>A
ABCC6 transcript variant X2 XM_017023212.1:c.2680= XM_017023212.1:c.2680G>A
ABCC6 transcript variant X8 XM_017023214.2:c.2848= XM_017023214.2:c.2848G>A
ABCC6 transcript variant X8 XM_017023214.1:c.2848= XM_017023214.1:c.2848G>A
ABCC6 transcript variant X3 XM_011522480.1:c.2506= XM_011522480.1:c.2506G>A
ABCC6 transcript variant X9 XM_047434069.1:c.2680= XM_047434069.1:c.2680G>A
ABCC6 transcript variant X1 XM_011522479.3:c.2815= XM_011522479.3:c.2815G>A
ABCC6 transcript variant X1 XM_011522479.2:c.2815= XM_011522479.2:c.2815G>A
ABCC6 transcript variant X6 XM_011522479.1:c.2815= XM_011522479.1:c.2815G>A
ATP-binding cassette sub-family C member 6 isoform 1 NP_001162.5:p.Ala950= NP_001162.5:p.Ala950Thr
ATP-binding cassette sub-family C member 6 isoform 3 NP_001338729.1:p.Ala836= NP_001338729.1:p.Ala836Thr
ATP-binding cassette sub-family C member 6 isoform X3 XP_011520783.1:p.Ala836= XP_011520783.1:p.Ala836Thr
ATP-binding cassette sub-family C member 6 isoform X2 XP_016878701.1:p.Ala894= XP_016878701.1:p.Ala894Thr
ATP-binding cassette sub-family C member 6 isoform X4 XP_016878703.1:p.Ala950= XP_016878703.1:p.Ala950Thr
ATP-binding cassette sub-family C member 6 isoform X3 XP_011520782.1:p.Ala836= XP_011520782.1:p.Ala836Thr
ATP-binding cassette sub-family C member 6 isoform X5 XP_047290025.1:p.Ala894= XP_047290025.1:p.Ala894Thr
ATP-binding cassette sub-family C member 6 isoform X1 XP_011520781.1:p.Ala939= XP_011520781.1:p.Ala939Thr
multidrug resistance-associated protein 6 isoform 1 NP_001162.4:p.Ala950= NP_001162.4:p.Ala950Thr
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#.

33 SubSNP, 9 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ABCC6-LOVD ss107794872 Feb 13, 2009 (130)
2 NHLBI-ESP ss342421900 May 09, 2011 (134)
3 EXOME_CHIP ss491505048 May 04, 2012 (137)
4 ILLUMINA ss780716309 Sep 08, 2015 (146)
5 ILLUMINA ss783391664 Sep 08, 2015 (146)
6 EVA_EXAC ss1692178070 Apr 01, 2015 (144)
7 ILLUMINA ss1752184027 Sep 08, 2015 (146)
8 ILLUMINA ss1917905011 Feb 12, 2016 (147)
9 ILLUMINA ss1946410315 Feb 12, 2016 (147)
10 ILLUMINA ss1959663787 Feb 12, 2016 (147)
11 HUMAN_LONGEVITY ss2211038066 Dec 20, 2016 (150)
12 GNOMAD ss2741786635 Nov 08, 2017 (151)
13 GNOMAD ss2749480937 Nov 08, 2017 (151)
14 GNOMAD ss2940928993 Nov 08, 2017 (151)
15 ILLUMINA ss3021689259 Nov 08, 2017 (151)
16 ILLUMINA ss3627490079 Oct 12, 2018 (152)
17 ILLUMINA ss3634634805 Oct 12, 2018 (152)
18 ILLUMINA ss3640342125 Oct 12, 2018 (152)
19 ILLUMINA ss3644663405 Oct 12, 2018 (152)
20 ILLUMINA ss3652095721 Oct 12, 2018 (152)
21 ILLUMINA ss3653834241 Oct 12, 2018 (152)
22 ILLUMINA ss3725548537 Jul 13, 2019 (153)
23 ILLUMINA ss3744429219 Jul 13, 2019 (153)
24 ILLUMINA ss3744935255 Jul 13, 2019 (153)
25 PAGE_CC ss3771869394 Jul 13, 2019 (153)
26 ILLUMINA ss3772433611 Jul 13, 2019 (153)
27 EVA ss3824992002 Apr 27, 2020 (154)
28 TOPMED ss5009588631 Apr 27, 2021 (155)
29 TOMMO_GENOMICS ss5218677116 Apr 27, 2021 (155)
30 EVA ss5422655397 Oct 17, 2022 (156)
31 TOMMO_GENOMICS ss5773232390 Oct 17, 2022 (156)
32 EVA ss5847765351 Oct 17, 2022 (156)
33 EVA ss5950002779 Oct 17, 2022 (156)
34 ExAC NC_000016.9 - 16263650 Oct 12, 2018 (152)
35 gnomAD - Genomes NC_000016.10 - 16169793 Apr 27, 2021 (155)
36 gnomAD - Exomes NC_000016.9 - 16263650 Jul 13, 2019 (153)
37 GO Exome Sequencing Project NC_000016.9 - 16263650 Oct 12, 2018 (152)
38 The PAGE Study NC_000016.10 - 16169793 Jul 13, 2019 (153)
39 8.3KJPN NC_000016.9 - 16263650 Apr 27, 2021 (155)
40 14KJPN NC_000016.10 - 16169793 Oct 17, 2022 (156)
41 TopMed NC_000016.10 - 16169793 Apr 27, 2021 (155)
42 ALFA NC_000016.10 - 16169793 Apr 27, 2021 (155)
43 ClinVar RCV000437137.5 Oct 17, 2022 (156)
44 ClinVar RCV000499095.4 Oct 17, 2022 (156)
45 ClinVar RCV002253430.1 Oct 17, 2022 (156)
46 ClinVar RCV002253431.1 Oct 17, 2022 (156)
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
2576571, 11064873, 1449189, 76646423, ss342421900, ss491505048, ss780716309, ss783391664, ss1692178070, ss1752184027, ss1917905011, ss1946410315, ss1959663787, ss2741786635, ss2749480937, ss2940928993, ss3021689259, ss3627490079, ss3634634805, ss3640342125, ss3644663405, ss3652095721, ss3653834241, ss3744429219, ss3744935255, ss3772433611, ss3824992002, ss5218677116, ss5422655397, ss5847765351, ss5950002779 NC_000016.9:16263649:C:T NC_000016.10:16169792:C:T (self)
RCV000437137.5, RCV000499095.4, RCV002253430.1, RCV002253431.1, 484393832, 1090863, 107069494, 225134292, 9817751804, ss107794872, ss2211038066, ss3725548537, ss3771869394, ss5009588631, ss5773232390 NC_000016.10:16169792:C:T NC_000016.10:16169792:C:T (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 rs72657689
PMID Title Author Year Journal
17617515 Mutation detection in the ABCC6 gene and genotype-phenotype analysis in a large international case series affected by pseudoxanthoma elasticum. Pfendner EG et al. 2007 Journal of medical genetics
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