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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.

rs4541628

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:26029013 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.310922 (82298/264690, TOPMED)
A=0.306236 (42696/139422, GnomAD)
G=0.46957 (13269/28258, 14KJPN) (+ 14 more)
G=0.46623 (7814/16760, 8.3KJPN)
A=0.33810 (5647/16702, ALFA)
A=0.3143 (2013/6404, 1000G_30x)
A=0.3237 (1621/5008, 1000G)
A=0.3904 (1749/4480, Estonian)
A=0.3734 (1439/3854, ALSPAC)
A=0.3741 (1387/3708, TWINSUK)
G=0.4160 (1219/2930, KOREAN)
G=0.4269 (782/1832, Korea1K)
A=0.385 (231/600, NorthernSweden)
G=0.379 (128/338, SGDP_PRJ)
A=0.194 (42/216, Qatari)
A=0.30 (12/40, GENOME_DK)
G=0.39 (15/38, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 16702 G=0.66190 A=0.33810
European Sub 12214 G=0.61675 A=0.38325
African Sub 2864 G=0.8687 A=0.1313
African Others Sub 108 G=0.889 A=0.111
African American Sub 2756 G=0.8679 A=0.1321
Asian Sub 108 G=0.389 A=0.611
East Asian Sub 84 G=0.35 A=0.65
Other Asian Sub 24 G=0.54 A=0.46
Latin American 1 Sub 146 G=0.685 A=0.315
Latin American 2 Sub 610 G=0.602 A=0.398
South Asian Sub 94 G=0.83 A=0.17
Other Sub 666 G=0.671 A=0.329


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=0.689078 A=0.310922
gnomAD - Genomes Global Study-wide 139422 G=0.693764 A=0.306236
gnomAD - Genomes European Sub 75388 G=0.63181 A=0.36819
gnomAD - Genomes African Sub 41900 G=0.85826 A=0.14174
gnomAD - Genomes American Sub 13548 G=0.61758 A=0.38242
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.6300 A=0.3700
gnomAD - Genomes East Asian Sub 3118 G=0.4015 A=0.5985
gnomAD - Genomes Other Sub 2146 G=0.6626 A=0.3374
14KJPN JAPANESE Study-wide 28258 G=0.46957 A=0.53043
8.3KJPN JAPANESE Study-wide 16760 G=0.46623 A=0.53377
Allele Frequency Aggregator Total Global 16702 G=0.66190 A=0.33810
Allele Frequency Aggregator European Sub 12214 G=0.61675 A=0.38325
Allele Frequency Aggregator African Sub 2864 G=0.8687 A=0.1313
Allele Frequency Aggregator Other Sub 666 G=0.671 A=0.329
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.602 A=0.398
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.685 A=0.315
Allele Frequency Aggregator Asian Sub 108 G=0.389 A=0.611
Allele Frequency Aggregator South Asian Sub 94 G=0.83 A=0.17
1000Genomes_30x Global Study-wide 6404 G=0.6857 A=0.3143
1000Genomes_30x African Sub 1786 G=0.9009 A=0.0991
1000Genomes_30x Europe Sub 1266 G=0.6603 A=0.3397
1000Genomes_30x South Asian Sub 1202 G=0.7296 A=0.2704
1000Genomes_30x East Asian Sub 1170 G=0.3726 A=0.6274
1000Genomes_30x American Sub 980 G=0.646 A=0.354
1000Genomes Global Study-wide 5008 G=0.6763 A=0.3237
1000Genomes African Sub 1322 G=0.8994 A=0.1006
1000Genomes East Asian Sub 1008 G=0.3690 A=0.6310
1000Genomes Europe Sub 1006 G=0.6600 A=0.3400
1000Genomes South Asian Sub 978 G=0.729 A=0.271
1000Genomes American Sub 694 G=0.647 A=0.353
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6096 A=0.3904
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6266 A=0.3734
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6259 A=0.3741
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.4160 A=0.5840, C=0.0000
Korean Genome Project KOREAN Study-wide 1832 G=0.4269 A=0.5731
Northern Sweden ACPOP Study-wide 600 G=0.615 A=0.385
SGDP_PRJ Global Study-wide 338 G=0.379 A=0.621
Qatari Global Study-wide 216 G=0.806 A=0.194
The Danish reference pan genome Danish Study-wide 40 G=0.70 A=0.30
Siberian Global Study-wide 38 G=0.39 A=0.61
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 5 NC_000005.10:g.26029013G>A
GRCh38.p14 chr 5 NC_000005.10:g.26029013G>C
GRCh37.p13 chr 5 NC_000005.9:g.26029122G>A
GRCh37.p13 chr 5 NC_000005.9:g.26029122G>C
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 G= A C
GRCh38.p14 chr 5 NC_000005.10:g.26029013= NC_000005.10:g.26029013G>A NC_000005.10:g.26029013G>C
GRCh37.p13 chr 5 NC_000005.9:g.26029122= NC_000005.9:g.26029122G>A NC_000005.9:g.26029122G>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#.

52 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss81466059 Dec 14, 2007 (130)
2 BGI ss105914317 Feb 04, 2009 (130)
3 1000GENOMES ss210604479 Jul 14, 2010 (132)
4 1000GENOMES ss221580070 Jul 14, 2010 (132)
5 1000GENOMES ss232872603 Jul 14, 2010 (132)
6 1000GENOMES ss240061761 Jul 15, 2010 (132)
7 GMI ss278214534 May 04, 2012 (137)
8 GMI ss285141804 Apr 25, 2013 (138)
9 SSMP ss652125051 Apr 25, 2013 (138)
10 EVA-GONL ss981367427 Aug 21, 2014 (142)
11 1000GENOMES ss1314345827 Aug 21, 2014 (142)
12 DDI ss1430282582 Apr 01, 2015 (144)
13 EVA_GENOME_DK ss1581059546 Apr 01, 2015 (144)
14 EVA_UK10K_ALSPAC ss1612505159 Apr 01, 2015 (144)
15 EVA_UK10K_TWINSUK ss1655499192 Apr 01, 2015 (144)
16 HAMMER_LAB ss1803241951 Sep 08, 2015 (146)
17 WEILL_CORNELL_DGM ss1924627332 Feb 12, 2016 (147)
18 GENOMED ss1970042452 Jul 19, 2016 (147)
19 JJLAB ss2022914150 Sep 14, 2016 (149)
20 USC_VALOUEV ss2151063413 Dec 20, 2016 (150)
21 HUMAN_LONGEVITY ss2272266362 Dec 20, 2016 (150)
22 SYSTEMSBIOZJU ss2625957013 Nov 08, 2017 (151)
23 GRF ss2706596873 Nov 08, 2017 (151)
24 GNOMAD ss2822414731 Nov 08, 2017 (151)
25 SWEGEN ss2996619183 Nov 08, 2017 (151)
26 BIOINF_KMB_FNS_UNIBA ss3025241319 Nov 08, 2017 (151)
27 CSHL ss3346298194 Nov 08, 2017 (151)
28 EGCUT_WGS ss3664508254 Jul 13, 2019 (153)
29 EVA_DECODE ss3714323879 Jul 13, 2019 (153)
30 ACPOP ss3732189595 Jul 13, 2019 (153)
31 EVA ss3763202380 Jul 13, 2019 (153)
32 KHV_HUMAN_GENOMES ss3806373547 Jul 13, 2019 (153)
33 EVA ss3829151767 Apr 26, 2020 (154)
34 EVA ss3838042709 Apr 26, 2020 (154)
35 EVA ss3843483269 Apr 26, 2020 (154)
36 SGDP_PRJ ss3861455476 Apr 26, 2020 (154)
37 KRGDB ss3907914450 Apr 26, 2020 (154)
38 KOGIC ss3956295928 Apr 26, 2020 (154)
39 TOPMED ss4653410042 Apr 26, 2021 (155)
40 TOMMO_GENOMICS ss5170880805 Apr 26, 2021 (155)
41 1000G_HIGH_COVERAGE ss5263271690 Oct 13, 2022 (156)
42 EVA ss5356367385 Oct 13, 2022 (156)
43 HUGCELL_USP ss5461573123 Oct 13, 2022 (156)
44 EVA ss5507953122 Oct 13, 2022 (156)
45 1000G_HIGH_COVERAGE ss5546537772 Oct 13, 2022 (156)
46 SANFORD_IMAGENETICS ss5637417727 Oct 13, 2022 (156)
47 TOMMO_GENOMICS ss5706691200 Oct 13, 2022 (156)
48 YY_MCH ss5806120053 Oct 13, 2022 (156)
49 EVA ss5834676194 Oct 13, 2022 (156)
50 EVA ss5854733778 Oct 13, 2022 (156)
51 EVA ss5893434429 Oct 13, 2022 (156)
52 EVA ss5965832907 Oct 13, 2022 (156)
53 1000Genomes NC_000005.9 - 26029122 Oct 12, 2018 (152)
54 1000Genomes_30x NC_000005.10 - 26029013 Oct 13, 2022 (156)
55 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 26029122 Oct 12, 2018 (152)
56 Genetic variation in the Estonian population NC_000005.9 - 26029122 Oct 12, 2018 (152)
57 The Danish reference pan genome NC_000005.9 - 26029122 Apr 26, 2020 (154)
58 gnomAD - Genomes NC_000005.10 - 26029013 Apr 26, 2021 (155)
59 KOREAN population from KRGDB NC_000005.9 - 26029122 Apr 26, 2020 (154)
60 Korean Genome Project NC_000005.10 - 26029013 Apr 26, 2020 (154)
61 Northern Sweden NC_000005.9 - 26029122 Jul 13, 2019 (153)
62 Qatari NC_000005.9 - 26029122 Apr 26, 2020 (154)
63 SGDP_PRJ NC_000005.9 - 26029122 Apr 26, 2020 (154)
64 Siberian NC_000005.9 - 26029122 Apr 26, 2020 (154)
65 8.3KJPN NC_000005.9 - 26029122 Apr 26, 2021 (155)
66 14KJPN NC_000005.10 - 26029013 Oct 13, 2022 (156)
67 TopMed NC_000005.10 - 26029013 Apr 26, 2021 (155)
68 UK 10K study - Twins NC_000005.9 - 26029122 Oct 12, 2018 (152)
69 ALFA NC_000005.10 - 26029013 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)
rs58057494 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81466059, ss210604479, ss278214534, ss285141804 NC_000005.8:26064878:G:A NC_000005.10:26029012:G:A (self)
25918618, 14420052, 10246502, 7224485, 15091844, 5474460, 6669262, 13472456, 3579767, 28850112, 14420052, ss221580070, ss232872603, ss240061761, ss652125051, ss981367427, ss1314345827, ss1430282582, ss1581059546, ss1612505159, ss1655499192, ss1803241951, ss1924627332, ss1970042452, ss2022914150, ss2151063413, ss2625957013, ss2706596873, ss2822414731, ss2996619183, ss3346298194, ss3664508254, ss3732189595, ss3763202380, ss3829151767, ss3838042709, ss3861455476, ss3907914450, ss5170880805, ss5356367385, ss5507953122, ss5637417727, ss5834676194, ss5965832907 NC_000005.9:26029121:G:A NC_000005.10:26029012:G:A (self)
34063707, 183137512, 12673929, 40528304, 490787599, 4218658611, ss2272266362, ss3025241319, ss3714323879, ss3806373547, ss3843483269, ss3956295928, ss4653410042, ss5263271690, ss5461573123, ss5546537772, ss5706691200, ss5806120053, ss5854733778, ss5893434429 NC_000005.10:26029012:G:A NC_000005.10:26029012:G:A (self)
ss105914317 NT_006576.16:26019121:G:A NC_000005.10:26029012:G:A (self)
15091844, ss3907914450 NC_000005.9:26029121:G:C NC_000005.10:26029012:G:C (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 rs4541628

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