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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.

rs75668586

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:95301707 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.002074 (549/264690, TOPMED)
G=0.001355 (190/140256, GnomAD)
G=0.07248 (2048/28256, 14KJPN) (+ 9 more)
G=0.00064 (12/18890, ALFA)
G=0.07359 (1233/16756, 8.3KJPN)
G=0.0086 (55/6404, 1000G_30x)
G=0.0070 (35/5008, 1000G)
G=0.0002 (1/4480, Estonian)
G=0.0556 (162/2916, KOREAN)
G=0.019 (4/214, Vietnamese)
A=0.5 (4/8, SGDP_PRJ)
G=0.5 (4/8, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ABCC4 : 2KB Upstream Variant
LOC102724149 : Intron 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 18890 A=0.99936 G=0.00064
European Sub 14286 A=0.99993 G=0.00007
African Sub 2946 A=1.0000 G=0.0000
African Others Sub 114 A=1.000 G=0.000
African American Sub 2832 A=1.0000 G=0.0000
Asian Sub 112 A=0.920 G=0.080
East Asian Sub 86 A=0.93 G=0.07
Other Asian Sub 26 A=0.88 G=0.12
Latin American 1 Sub 146 A=1.000 G=0.000
Latin American 2 Sub 610 A=1.000 G=0.000
South Asian Sub 98 A=1.00 G=0.00
Other Sub 692 A=0.997 G=0.003


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 A=0.997926 G=0.002074
gnomAD - Genomes Global Study-wide 140256 A=0.998645 G=0.001355
gnomAD - Genomes European Sub 75928 A=0.99999 G=0.00001
gnomAD - Genomes African Sub 42066 A=0.99964 G=0.00036
gnomAD - Genomes American Sub 13664 A=0.99934 G=0.00066
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3124 A=0.9481 G=0.0519
gnomAD - Genomes Other Sub 2154 A=0.9986 G=0.0014
14KJPN JAPANESE Study-wide 28256 A=0.92752 G=0.07248
Allele Frequency Aggregator Total Global 18890 A=0.99936 G=0.00064
Allele Frequency Aggregator European Sub 14286 A=0.99993 G=0.00007
Allele Frequency Aggregator African Sub 2946 A=1.0000 G=0.0000
Allele Frequency Aggregator Other Sub 692 A=0.997 G=0.003
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 112 A=0.920 G=0.080
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
8.3KJPN JAPANESE Study-wide 16756 A=0.92641 G=0.07359
1000Genomes_30x Global Study-wide 6404 A=0.9914 G=0.0086
1000Genomes_30x African Sub 1786 A=1.0000 G=0.0000
1000Genomes_30x Europe Sub 1266 A=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 A=0.9992 G=0.0008
1000Genomes_30x East Asian Sub 1170 A=0.9538 G=0.0462
1000Genomes_30x American Sub 980 A=1.000 G=0.000
1000Genomes Global Study-wide 5008 A=0.9930 G=0.0070
1000Genomes African Sub 1322 A=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 A=0.9663 G=0.0337
1000Genomes Europe Sub 1006 A=1.0000 G=0.0000
1000Genomes South Asian Sub 978 A=0.999 G=0.001
1000Genomes American Sub 694 A=1.000 G=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9998 G=0.0002
KOREAN population from KRGDB KOREAN Study-wide 2916 A=0.9444 G=0.0556
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.981 G=0.019
SGDP_PRJ Global Study-wide 8 A=0.5 G=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 13 NC_000013.11:g.95301707A>G
GRCh37.p13 chr 13 NC_000013.10:g.95953961A>G
PEL blood group RefSeqGene (LRG_1183) NG_050651.2:g.4740T>C
Gene: ABCC4, ATP binding cassette subfamily C member 4 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
ABCC4 transcript variant 2 NM_001105515.3:c. N/A Upstream Transcript Variant
ABCC4 transcript variant 3 NM_001301829.2:c. N/A Upstream Transcript Variant
ABCC4 transcript variant 4 NM_001301830.2:c. N/A Upstream Transcript Variant
ABCC4 transcript variant 1 NM_005845.5:c. N/A Upstream Transcript Variant
ABCC4 transcript variant X3 XM_017020320.3:c. N/A Upstream Transcript Variant
ABCC4 transcript variant X1 XM_047430034.1:c. N/A N/A
ABCC4 transcript variant X2 XM_047430035.1:c. N/A N/A
Gene: LOC102724149, uncharacterized LOC102724149 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC102724149 transcript variant X2 XR_007063837.1:n. N/A Intron Variant
LOC102724149 transcript variant X1 XR_429273.4: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
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 A= G
GRCh38.p14 chr 13 NC_000013.11:g.95301707= NC_000013.11:g.95301707A>G
GRCh37.p13 chr 13 NC_000013.10:g.95953961= NC_000013.10:g.95953961A>G
PEL blood group RefSeqGene (LRG_1183) NG_050651.2:g.4740= NG_050651.2:g.4740T>C
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#.

24 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 BGI ss103150396 Dec 01, 2009 (131)
2 1000GENOMES ss242852194 Jul 15, 2010 (132)
3 SSMP ss659494903 Apr 25, 2013 (138)
4 1000GENOMES ss1349479192 Aug 21, 2014 (142)
5 HUMAN_LONGEVITY ss2198974316 Dec 20, 2016 (150)
6 GRF ss2700582885 Nov 08, 2017 (151)
7 GNOMAD ss2923253264 Nov 08, 2017 (151)
8 EGCUT_WGS ss3678823823 Jul 13, 2019 (153)
9 EVA ss3751852007 Jul 13, 2019 (153)
10 KHV_HUMAN_GENOMES ss3817183978 Jul 13, 2019 (153)
11 SGDP_PRJ ss3880642059 Apr 27, 2020 (154)
12 KRGDB ss3929562278 Apr 27, 2020 (154)
13 TOPMED ss4957680525 Apr 26, 2021 (155)
14 TOMMO_GENOMICS ss5211425145 Apr 26, 2021 (155)
15 1000G_HIGH_COVERAGE ss5294837278 Oct 16, 2022 (156)
16 EVA ss5412781774 Oct 16, 2022 (156)
17 HUGCELL_USP ss5489090651 Oct 16, 2022 (156)
18 1000G_HIGH_COVERAGE ss5594427030 Oct 16, 2022 (156)
19 SANFORD_IMAGENETICS ss5655417425 Oct 16, 2022 (156)
20 TOMMO_GENOMICS ss5763691453 Oct 16, 2022 (156)
21 YY_MCH ss5814394503 Oct 16, 2022 (156)
22 EVA ss5850869058 Oct 16, 2022 (156)
23 EVA ss5926368211 Oct 16, 2022 (156)
24 EVA ss5946856371 Oct 16, 2022 (156)
25 1000Genomes NC_000013.10 - 95953961 Oct 12, 2018 (152)
26 1000Genomes_30x NC_000013.11 - 95301707 Oct 16, 2022 (156)
27 Genetic variation in the Estonian population NC_000013.10 - 95953961 Oct 12, 2018 (152)
28 gnomAD - Genomes NC_000013.11 - 95301707 Apr 26, 2021 (155)
29 KOREAN population from KRGDB NC_000013.10 - 95953961 Apr 27, 2020 (154)
30 SGDP_PRJ NC_000013.10 - 95953961 Apr 27, 2020 (154)
31 8.3KJPN NC_000013.10 - 95953961 Apr 26, 2021 (155)
32 14KJPN NC_000013.11 - 95301707 Oct 16, 2022 (156)
33 TopMed NC_000013.11 - 95301707 Apr 26, 2021 (155)
34 A Vietnamese Genetic Variation Database NC_000013.10 - 95953961 Jul 13, 2019 (153)
35 ALFA NC_000013.11 - 95301707 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
62401579, 24562071, 36739672, 32659039, 69394452, 7707660, ss242852194, ss659494903, ss1349479192, ss2700582885, ss2923253264, ss3678823823, ss3751852007, ss3880642059, ss3929562278, ss5211425145, ss5412781774, ss5655417425, ss5946856371 NC_000013.10:95953960:A:G NC_000013.11:95301706:A:G (self)
81952965, 440066531, 97528557, 173226183, 984186665, ss2198974316, ss3817183978, ss4957680525, ss5294837278, ss5489090651, ss5594427030, ss5763691453, ss5814394503, ss5850869058, ss5926368211 NC_000013.11:95301706:A:G NC_000013.11:95301706:A:G (self)
ss103150396 NT_009952.14:9043636:A:G NC_000013.11:95301706:A:G (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 rs75668586

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