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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.

rs10475542

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr5:170352947 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.035011 (9267/264690, TOPMED)
G=0.033322 (4673/140238, GnomAD)
G=0.009211 (1202/130500, ALFA) (+ 7 more)
G=0.0355 (178/5008, 1000G)
G=0.0000 (0/3854, ALSPAC)
G=0.0003 (1/3708, TWINSUK)
G=0.073 (73/996, HapMap)
G=0.002 (1/626, Chileans)
G=0.009 (2/216, Qatari)
A=0.41 (9/22, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KCNIP1 : 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.p13 chr 5 NC_000005.10:g.170352947A>G
GRCh37.p13 chr 5 NC_000005.9:g.169779951A>G
KCNIP1 RefSeqGene NG_011538.2:g.4071A>G
Gene: KCNIP1, potassium voltage-gated channel interacting protein 1 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
KCNIP1 transcript variant 3 NM_001034838.3:c. N/A Upstream Transcript Variant
KCNIP1 transcript variant 1 NM_001034837.3:c. N/A N/A
KCNIP1 transcript variant 5 NM_001278339.2:c. N/A N/A
KCNIP1 transcript variant 4 NM_001278340.2:c. N/A N/A
KCNIP1 transcript variant 2 NM_014592.4:c. N/A N/A
KCNIP1 transcript variant X1 XM_017009407.1:c. N/A Upstream Transcript Variant
KCNIP1 transcript variant X2 XM_017009408.1: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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 130500 A=0.990789 G=0.009211
European Sub 110684 A=0.999557 G=0.000443
African Sub 9928 A=0.8933 G=0.1067
African Others Sub 334 A=0.850 G=0.150
African American Sub 9594 A=0.8948 G=0.1052
Asian Sub 668 A=1.000 G=0.000
East Asian Sub 506 A=1.000 G=0.000
Other Asian Sub 162 A=1.000 G=0.000
Latin American 1 Sub 742 A=0.980 G=0.020
Latin American 2 Sub 2352 A=0.9953 G=0.0047
South Asian Sub 196 A=1.000 G=0.000
Other Sub 5930 A=0.9885 G=0.0115


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=0.964989 G=0.035011
gnomAD - Genomes Global Study-wide 140238 A=0.966678 G=0.033322
gnomAD - Genomes European Sub 75948 A=0.99964 G=0.00036
gnomAD - Genomes African Sub 42016 A=0.89406 G=0.10594
gnomAD - Genomes American Sub 13664 A=0.99019 G=0.00981
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.9991 G=0.0009
gnomAD - Genomes East Asian Sub 3134 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 A=0.9731 G=0.0269
1000Genomes Global Study-wide 5008 A=0.9645 G=0.0355
1000Genomes African Sub 1322 A=0.8691 G=0.1309
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=1.0000 G=0.0000
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.993 G=0.007
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=1.0000 G=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9997 G=0.0003
HapMap Global Study-wide 996 A=0.927 G=0.073
HapMap African Sub 692 A=0.912 G=0.088
HapMap American Sub 214 A=0.944 G=0.056
HapMap Asian Sub 90 A=1.00 G=0.00
Chileans Chilean Study-wide 626 A=0.998 G=0.002
Qatari Global Study-wide 216 A=0.991 G=0.009
SGDP_PRJ Global Study-wide 22 A=0.41 G=0.59
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.p13 chr 5 NC_000005.10:g.170352947= NC_000005.10:g.170352947A>G
GRCh37.p13 chr 5 NC_000005.9:g.169779951= NC_000005.9:g.169779951A>G
KCNIP1 RefSeqGene NG_011538.2:g.4071= NG_011538.2:g.4071A>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#.

51 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss14848525 Dec 05, 2003 (119)
2 ILLUMINA ss74855131 Dec 07, 2007 (129)
3 AFFY ss76623763 Dec 07, 2007 (129)
4 HGSV ss84667308 Dec 15, 2007 (130)
5 1000GENOMES ss113652954 Jan 25, 2009 (130)
6 ILLUMINA-UK ss116905185 Feb 14, 2009 (130)
7 KRIBB_YJKIM ss119623171 Dec 01, 2009 (131)
8 ILLUMINA ss159897433 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss166221458 Jul 04, 2010 (132)
10 ILLUMINA ss170129783 Jul 04, 2010 (132)
11 BUSHMAN ss201199314 Jul 04, 2010 (132)
12 1000GENOMES ss222113629 Jul 14, 2010 (132)
13 ILLUMINA ss479276995 May 04, 2012 (137)
14 ILLUMINA ss479279977 May 04, 2012 (137)
15 ILLUMINA ss479655589 Sep 08, 2015 (146)
16 ILLUMINA ss484439048 May 04, 2012 (137)
17 ILLUMINA ss536608460 Sep 08, 2015 (146)
18 TISHKOFF ss558885601 Apr 25, 2013 (138)
19 ILLUMINA ss778356975 Sep 08, 2015 (146)
20 ILLUMINA ss782666010 Sep 08, 2015 (146)
21 ILLUMINA ss783634803 Sep 08, 2015 (146)
22 ILLUMINA ss831916604 Sep 08, 2015 (146)
23 ILLUMINA ss833811726 Sep 08, 2015 (146)
24 JMKIDD_LAB ss1073253418 Aug 21, 2014 (142)
25 1000GENOMES ss1318306638 Aug 21, 2014 (142)
26 EVA_UK10K_ALSPAC ss1614600454 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1657594487 Apr 01, 2015 (144)
28 ILLUMINA ss1752563416 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1925655979 Feb 12, 2016 (147)
30 HUMAN_LONGEVITY ss2280454536 Dec 20, 2016 (150)
31 TOPMED ss2448783772 Dec 20, 2016 (150)
32 ILLUMINA ss2634375333 Nov 08, 2017 (151)
33 GNOMAD ss2833893601 Nov 08, 2017 (151)
34 TOPMED ss3485835767 Nov 08, 2017 (151)
35 ILLUMINA ss3629402775 Oct 12, 2018 (152)
36 ILLUMINA ss3632296877 Oct 12, 2018 (152)
37 ILLUMINA ss3633399492 Oct 12, 2018 (152)
38 ILLUMINA ss3634121088 Oct 12, 2018 (152)
39 ILLUMINA ss3635035508 Oct 12, 2018 (152)
40 ILLUMINA ss3635802587 Oct 12, 2018 (152)
41 ILLUMINA ss3636749316 Oct 12, 2018 (152)
42 ILLUMINA ss3637555275 Oct 12, 2018 (152)
43 ILLUMINA ss3638596417 Oct 12, 2018 (152)
44 ILLUMINA ss3640742802 Oct 12, 2018 (152)
45 ILLUMINA ss3643539045 Oct 12, 2018 (152)
46 ILLUMINA ss3745335667 Jul 13, 2019 (153)
47 ILLUMINA ss3772829545 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3807563825 Jul 13, 2019 (153)
49 SGDP_PRJ ss3863541798 Apr 26, 2020 (154)
50 EVA ss4017245716 Apr 26, 2021 (155)
51 TOPMED ss4688240409 Apr 26, 2021 (155)
52 1000Genomes NC_000005.9 - 169779951 Oct 12, 2018 (152)
53 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 169779951 Oct 12, 2018 (152)
54 Chileans NC_000005.9 - 169779951 Apr 26, 2020 (154)
55 gnomAD - Genomes NC_000005.10 - 170352947 Apr 26, 2021 (155)
56 HapMap NC_000005.10 - 170352947 Apr 26, 2020 (154)
57 Qatari NC_000005.9 - 169779951 Apr 26, 2020 (154)
58 SGDP_PRJ NC_000005.9 - 169779951 Apr 26, 2020 (154)
59 TopMed NC_000005.10 - 170352947 Apr 26, 2021 (155)
60 UK 10K study - Twins NC_000005.9 - 169779951 Oct 12, 2018 (152)
61 ALFA NC_000005.10 - 170352947 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).

Associated ID History Updated (Build)
rs58549158 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84667308, ss113652954, ss116905185, ss166221458, ss201199314, ss479276995, ss3643539045 NC_000005.8:169712528:A:G NC_000005.10:170352946:A:G (self)
30023774, 16715422, 366318, 7697909, 15558778, 16715422, ss222113629, ss479279977, ss479655589, ss484439048, ss536608460, ss558885601, ss778356975, ss782666010, ss783634803, ss831916604, ss833811726, ss1073253418, ss1318306638, ss1614600454, ss1657594487, ss1752563416, ss1925655979, ss2448783772, ss2634375333, ss2833893601, ss3629402775, ss3632296877, ss3633399492, ss3634121088, ss3635035508, ss3635802587, ss3636749316, ss3637555275, ss3638596417, ss3640742802, ss3745335667, ss3772829545, ss3863541798, ss4017245716 NC_000005.9:169779950:A:G NC_000005.10:170352946:A:G (self)
212357964, 3025485, 328686194, 525617966, 8408791758, ss2280454536, ss3485835767, ss3807563825, ss4688240409 NC_000005.10:170352946:A:G NC_000005.10:170352946:A:G (self)
ss14848525 NT_023133.11:14589508:A:G NC_000005.10:170352946:A:G (self)
ss74855131, ss76623763, ss119623171, ss159897433, ss170129783 NT_023133.13:14591223:A:G NC_000005.10:170352946: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 rs10475542

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