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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.

rs58872553

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:43392 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.147331 (38997/264690, TOPMED)
C=0.144876 (20307/140168, GnomAD)
C=0.14484 (2736/18890, ALFA) (+ 12 more)
C=0.1140 (730/6404, 1000G_30x)
C=0.1092 (547/5008, 1000G)
C=0.1154 (517/4480, Estonian)
C=0.1461 (563/3854, ALSPAC)
C=0.1556 (577/3708, TWINSUK)
C=0.167 (167/998, GoNL)
C=0.167 (100/600, NorthernSweden)
C=0.234 (50/214, Qatari)
T=0.446 (50/112, SGDP_PRJ)
C=0.17 (7/40, GENOME_DK)
T=0.5 (2/4, Siberian)
C=0.5 (2/4, 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 18890 T=0.85516 C=0.14484
European Sub 14286 T=0.85069 C=0.14931
African Sub 2946 T=0.8669 C=0.1331
African Others Sub 114 T=0.877 C=0.123
African American Sub 2832 T=0.8665 C=0.1335
Asian Sub 112 T=0.991 C=0.009
East Asian Sub 86 T=0.99 C=0.01
Other Asian Sub 26 T=1.00 C=0.00
Latin American 1 Sub 146 T=0.788 C=0.212
Latin American 2 Sub 610 T=0.877 C=0.123
South Asian Sub 98 T=0.95 C=0.05
Other Sub 692 T=0.857 C=0.143


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 T=0.852669 C=0.147331
gnomAD - Genomes Global Study-wide 140168 T=0.855124 C=0.144876
gnomAD - Genomes European Sub 75934 T=0.85208 C=0.14792
gnomAD - Genomes African Sub 41988 T=0.85670 C=0.14330
gnomAD - Genomes American Sub 13644 T=0.85906 C=0.14094
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.7574 C=0.2426
gnomAD - Genomes East Asian Sub 3132 T=0.9990 C=0.0010
gnomAD - Genomes Other Sub 2148 T=0.8482 C=0.1518
Allele Frequency Aggregator Total Global 18890 T=0.85516 C=0.14484
Allele Frequency Aggregator European Sub 14286 T=0.85069 C=0.14931
Allele Frequency Aggregator African Sub 2946 T=0.8669 C=0.1331
Allele Frequency Aggregator Other Sub 692 T=0.857 C=0.143
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.877 C=0.123
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.788 C=0.212
Allele Frequency Aggregator Asian Sub 112 T=0.991 C=0.009
Allele Frequency Aggregator South Asian Sub 98 T=0.95 C=0.05
1000Genomes_30x Global Study-wide 6404 T=0.8860 C=0.1140
1000Genomes_30x African Sub 1786 T=0.8270 C=0.1730
1000Genomes_30x Europe Sub 1266 T=0.8365 C=0.1635
1000Genomes_30x South Asian Sub 1202 T=0.9260 C=0.0740
1000Genomes_30x East Asian Sub 1170 T=1.0000 C=0.0000
1000Genomes_30x American Sub 980 T=0.872 C=0.128
1000Genomes Global Study-wide 5008 T=0.8908 C=0.1092
1000Genomes African Sub 1322 T=0.8321 C=0.1679
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=0.8429 C=0.1571
1000Genomes South Asian Sub 978 T=0.927 C=0.073
1000Genomes American Sub 694 T=0.862 C=0.138
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.8846 C=0.1154
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8539 C=0.1461
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8444 C=0.1556
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.833 C=0.167
Northern Sweden ACPOP Study-wide 600 T=0.833 C=0.167
Qatari Global Study-wide 214 T=0.766 C=0.234
SGDP_PRJ Global Study-wide 112 T=0.446 C=0.554
The Danish reference pan genome Danish Study-wide 40 T=0.82 C=0.17
Siberian Global Study-wide 4 T=0.5 C=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 16 NC_000016.10:g.43392T>C
GRCh37.p13 chr 16 NC_000016.9:g.93392T>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 T= C
GRCh38.p14 chr 16 NC_000016.10:g.43392= NC_000016.10:g.43392T>C
GRCh37.p13 chr 16 NC_000016.9:g.93392= NC_000016.9:g.93392T>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#.

42 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss80962591 Dec 15, 2007 (129)
2 HGSV ss86093355 Dec 15, 2007 (129)
3 ILLUMINA-UK ss118150401 Feb 14, 2009 (130)
4 1000GENOMES ss227085835 Jul 14, 2010 (132)
5 1000GENOMES ss236913598 Jul 15, 2010 (132)
6 TISHKOFF ss564710063 Apr 25, 2013 (138)
7 SSMP ss660454738 Apr 25, 2013 (138)
8 EVA-GONL ss992173299 Aug 21, 2014 (142)
9 JMKIDD_LAB ss1080408326 Aug 21, 2014 (142)
10 1000GENOMES ss1354951086 Aug 21, 2014 (142)
11 DDI ss1427745442 Apr 01, 2015 (144)
12 EVA_GENOME_DK ss1577790936 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1633790868 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1676784901 Apr 01, 2015 (144)
15 EVA_DECODE ss1696205856 Apr 01, 2015 (144)
16 WEILL_CORNELL_DGM ss1935578347 Feb 12, 2016 (147)
17 JJLAB ss2028576465 Sep 14, 2016 (149)
18 USC_VALOUEV ss2156983796 Nov 08, 2017 (151)
19 HUMAN_LONGEVITY ss2209766500 Dec 20, 2016 (150)
20 GNOMAD ss2939123460 Nov 08, 2017 (151)
21 SWEGEN ss3013892171 Nov 08, 2017 (151)
22 BIOINF_KMB_FNS_UNIBA ss3028112990 Nov 08, 2017 (151)
23 CSHL ss3351285378 Nov 08, 2017 (151)
24 EGCUT_WGS ss3681020667 Jul 13, 2019 (153)
25 EVA_DECODE ss3698629208 Jul 13, 2019 (153)
26 ACPOP ss3741245937 Jul 13, 2019 (153)
27 EVA ss3753552333 Jul 13, 2019 (153)
28 PACBIO ss3787952304 Jul 13, 2019 (153)
29 PACBIO ss3792948376 Jul 13, 2019 (153)
30 PACBIO ss3797833117 Jul 13, 2019 (153)
31 KHV_HUMAN_GENOMES ss3818854546 Jul 13, 2019 (153)
32 EVA ss3834421863 Apr 27, 2020 (154)
33 SGDP_PRJ ss3883708616 Apr 27, 2020 (154)
34 TOPMED ss5004237784 Apr 26, 2021 (155)
35 1000G_HIGH_COVERAGE ss5299753644 Oct 16, 2022 (156)
36 EVA ss5421630821 Oct 16, 2022 (156)
37 HUGCELL_USP ss5493331046 Oct 16, 2022 (156)
38 1000G_HIGH_COVERAGE ss5601805282 Oct 16, 2022 (156)
39 SANFORD_IMAGENETICS ss5658253233 Oct 16, 2022 (156)
40 EVA ss5845956256 Oct 16, 2022 (156)
41 EVA ss5897860961 Oct 16, 2022 (156)
42 EVA ss5949680495 Oct 16, 2022 (156)
43 1000Genomes NC_000016.9 - 93392 Oct 12, 2018 (152)
44 1000Genomes_30x NC_000016.10 - 43392 Oct 16, 2022 (156)
45 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 93392 Oct 12, 2018 (152)
46 Genetic variation in the Estonian population NC_000016.9 - 93392 Oct 12, 2018 (152)
47 The Danish reference pan genome NC_000016.9 - 93392 Apr 27, 2020 (154)
48 gnomAD - Genomes NC_000016.10 - 43392 Apr 26, 2021 (155)
49 Genome of the Netherlands Release 5 NC_000016.9 - 93392 Apr 27, 2020 (154)
50 Northern Sweden NC_000016.9 - 93392 Jul 13, 2019 (153)
51 Qatari NC_000016.9 - 93392 Apr 27, 2020 (154)
52 SGDP_PRJ NC_000016.9 - 93392 Apr 27, 2020 (154)
53 Siberian NC_000016.9 - 93392 Apr 27, 2020 (154)
54 TopMed NC_000016.10 - 43392 Apr 26, 2021 (155)
55 UK 10K study - Twins NC_000016.9 - 93392 Oct 12, 2018 (152)
56 ALFA NC_000016.10 - 43392 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
ss80962591, ss86093355, ss118150401, ss1696205856 NC_000016.8:33391:T:C NC_000016.10:43391:T:C (self)
68075678, 37808194, 26758915, 4008351, 16869897, 14530802, 17620269, 35725596, 9500150, 37808194, ss227085835, ss236913598, ss564710063, ss660454738, ss992173299, ss1080408326, ss1354951086, ss1427745442, ss1577790936, ss1633790868, ss1676784901, ss1935578347, ss2028576465, ss2156983796, ss2939123460, ss3013892171, ss3351285378, ss3681020667, ss3741245937, ss3753552333, ss3787952304, ss3792948376, ss3797833117, ss3834421863, ss3883708616, ss5421630821, ss5658253233, ss5845956256, ss5949680495 NC_000016.9:93391:T:C NC_000016.10:43391:T:C (self)
89331217, 479814162, 219783445, 13515190598, ss2209766500, ss3028112990, ss3698629208, ss3818854546, ss5004237784, ss5299753644, ss5493331046, ss5601805282, ss5897860961 NC_000016.10:43391:T:C NC_000016.10:43391:T: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 rs58872553

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