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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs77592861

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:16569879 (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=0.042827 (11336/264690, TOPMED)
A=0.052090 (7304/140220, GnomAD)
A=0.00878 (248/28258, 14KJPN) (+ 17 more)
A=0.03212 (574/17868, ALFA)
A=0.00895 (150/16760, 8.3KJPN)
A=0.0426 (273/6404, 1000G_30x)
A=0.0463 (232/5008, 1000G)
A=0.0799 (358/4480, Estonian)
A=0.0701 (270/3854, ALSPAC)
A=0.0596 (221/3708, TWINSUK)
A=0.0205 (60/2922, KOREAN)
A=0.0218 (40/1832, Korea1K)
A=0.074 (74/998, GoNL)
A=0.060 (36/600, NorthernSweden)
A=0.046 (10/216, Qatari)
A=0.009 (2/212, Vietnamese)
G=0.48 (21/44, SGDP_PRJ)
A=0.12 (5/40, GENOME_DK)
G=0.5 (4/8, Siberian)
A=0.5 (4/8, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC35E1 : 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 17868 G=0.96788 A=0.03212, C=0.00000
European Sub 13484 G=0.96003 A=0.03997, C=0.00000
African Sub 2838 G=0.9926 A=0.0074, C=0.0000
African Others Sub 112 G=0.991 A=0.009, C=0.000
African American Sub 2726 G=0.9927 A=0.0073, C=0.0000
Asian Sub 108 G=1.000 A=0.000, C=0.000
East Asian Sub 82 G=1.00 A=0.00, C=0.00
Other Asian Sub 26 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 140 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 582 G=1.000 A=0.000, C=0.000
South Asian Sub 78 G=1.00 A=0.00, C=0.00
Other Sub 638 G=0.978 A=0.022, C=0.000


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=0.957173 A=0.042827
gnomAD - Genomes Global Study-wide 140220 G=0.947910 A=0.052090
gnomAD - Genomes European Sub 75926 G=0.92765 A=0.07235
gnomAD - Genomes African Sub 42026 G=0.97287 A=0.02713
gnomAD - Genomes American Sub 13658 G=0.97379 A=0.02621
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9582 A=0.0418
gnomAD - Genomes East Asian Sub 3134 G=0.9726 A=0.0274
gnomAD - Genomes Other Sub 2152 G=0.9591 A=0.0409
14KJPN JAPANESE Study-wide 28258 G=0.99122 A=0.00878
Allele Frequency Aggregator Total Global 17868 G=0.96788 A=0.03212, C=0.00000
Allele Frequency Aggregator European Sub 13484 G=0.96003 A=0.03997, C=0.00000
Allele Frequency Aggregator African Sub 2838 G=0.9926 A=0.0074, C=0.0000
Allele Frequency Aggregator Other Sub 638 G=0.978 A=0.022, C=0.000
Allele Frequency Aggregator Latin American 2 Sub 582 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 140 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 78 G=1.00 A=0.00, C=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.99105 A=0.00895
1000Genomes_30x Global Study-wide 6404 G=0.9574 A=0.0426
1000Genomes_30x African Sub 1786 G=0.9742 A=0.0258
1000Genomes_30x Europe Sub 1266 G=0.9336 A=0.0664
1000Genomes_30x South Asian Sub 1202 G=0.9301 A=0.0699
1000Genomes_30x East Asian Sub 1170 G=0.9735 A=0.0265
1000Genomes_30x American Sub 980 G=0.971 A=0.029
1000Genomes Global Study-wide 5008 G=0.9537 A=0.0463
1000Genomes African Sub 1322 G=0.9705 A=0.0295
1000Genomes East Asian Sub 1008 G=0.9742 A=0.0258
1000Genomes Europe Sub 1006 G=0.9294 A=0.0706
1000Genomes South Asian Sub 978 G=0.923 A=0.077
1000Genomes American Sub 694 G=0.970 A=0.030
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9201 A=0.0799
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9299 A=0.0701
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9404 A=0.0596
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9795 A=0.0205
Korean Genome Project KOREAN Study-wide 1832 G=0.9782 A=0.0218
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.926 A=0.074
Northern Sweden ACPOP Study-wide 600 G=0.940 A=0.060
Qatari Global Study-wide 216 G=0.954 A=0.046
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.991 A=0.009
SGDP_PRJ Global Study-wide 44 G=0.48 A=0.52
The Danish reference pan genome Danish Study-wide 40 G=0.88 A=0.12
Siberian Global Study-wide 8 G=0.5 A=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 19 NC_000019.10:g.16569879G>A
GRCh38.p14 chr 19 NC_000019.10:g.16569879G>C
GRCh37.p13 chr 19 NC_000019.9:g.16680690G>A
GRCh37.p13 chr 19 NC_000019.9:g.16680690G>C
CALR3 RefSeqGene (LRG_422) NG_031959.2:g.63326C>T
CALR3 RefSeqGene (LRG_422) NG_031959.2:g.63326C>G
Gene: SLC35E1, solute carrier family 35 member E1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC35E1 transcript NM_024881.5:c.492+1633C>T 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 G= A C
GRCh38.p14 chr 19 NC_000019.10:g.16569879= NC_000019.10:g.16569879G>A NC_000019.10:g.16569879G>C
GRCh37.p13 chr 19 NC_000019.9:g.16680690= NC_000019.9:g.16680690G>A NC_000019.9:g.16680690G>C
CALR3 RefSeqGene (LRG_422) NG_031959.2:g.63326= NG_031959.2:g.63326C>T NG_031959.2:g.63326C>G
SLC35E1 transcript NM_024881.4:c.492+1633= NM_024881.4:c.492+1633C>T NM_024881.4:c.492+1633C>G
SLC35E1 transcript NM_024881.5:c.492+1633= NM_024881.5:c.492+1633C>T NM_024881.5:c.492+1633C>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#.

43 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss237617600 Jul 15, 2010 (132)
2 1000GENOMES ss243836536 Jul 15, 2010 (132)
3 TISHKOFF ss565882966 Apr 25, 2013 (138)
4 SSMP ss661739091 Apr 25, 2013 (138)
5 EVA-GONL ss994135090 Aug 21, 2014 (142)
6 JMKIDD_LAB ss1081788947 Aug 21, 2014 (142)
7 1000GENOMES ss1362535866 Aug 21, 2014 (142)
8 DDI ss1428350164 Apr 01, 2015 (144)
9 EVA_GENOME_DK ss1578574313 Apr 01, 2015 (144)
10 EVA_UK10K_ALSPAC ss1637652070 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1680646103 Apr 01, 2015 (144)
12 EVA_DECODE ss1698194605 Apr 01, 2015 (144)
13 WEILL_CORNELL_DGM ss1937621707 Feb 12, 2016 (147)
14 JJLAB ss2029583759 Sep 14, 2016 (149)
15 USC_VALOUEV ss2158111077 Dec 20, 2016 (150)
16 HUMAN_LONGEVITY ss2224655885 Dec 20, 2016 (150)
17 GRF ss2702716148 Nov 08, 2017 (151)
18 GNOMAD ss2961005955 Nov 08, 2017 (151)
19 SWEGEN ss3017181969 Nov 08, 2017 (151)
20 CSHL ss3352221070 Nov 08, 2017 (151)
21 BIOINF_KMB_FNS_UNIBA ss3645511158 Oct 12, 2018 (152)
22 EGCUT_WGS ss3684003953 Jul 13, 2019 (153)
23 EVA_DECODE ss3702444556 Jul 13, 2019 (153)
24 ACPOP ss3742897202 Jul 13, 2019 (153)
25 EVA ss3755867405 Jul 13, 2019 (153)
26 KHV_HUMAN_GENOMES ss3821121855 Jul 13, 2019 (153)
27 EVA ss3835377507 Apr 27, 2020 (154)
28 SGDP_PRJ ss3887869531 Apr 27, 2020 (154)
29 KRGDB ss3937865833 Apr 27, 2020 (154)
30 KOGIC ss3980954721 Apr 27, 2020 (154)
31 TOPMED ss5069523193 Apr 27, 2021 (155)
32 TOMMO_GENOMICS ss5226983550 Apr 27, 2021 (155)
33 1000G_HIGH_COVERAGE ss5306671370 Oct 13, 2022 (156)
34 EVA ss5433856499 Oct 13, 2022 (156)
35 HUGCELL_USP ss5499276182 Oct 13, 2022 (156)
36 1000G_HIGH_COVERAGE ss5612137938 Oct 13, 2022 (156)
37 SANFORD_IMAGENETICS ss5662072371 Oct 13, 2022 (156)
38 TOMMO_GENOMICS ss5785347611 Oct 13, 2022 (156)
39 YY_MCH ss5817451061 Oct 13, 2022 (156)
40 EVA ss5840323321 Oct 13, 2022 (156)
41 EVA ss5852223984 Oct 13, 2022 (156)
42 EVA ss5927481658 Oct 13, 2022 (156)
43 EVA ss5953490288 Oct 13, 2022 (156)
44 1000Genomes NC_000019.9 - 16680690 Oct 12, 2018 (152)
45 1000Genomes_30x NC_000019.10 - 16569879 Oct 13, 2022 (156)
46 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 16680690 Oct 12, 2018 (152)
47 Genetic variation in the Estonian population NC_000019.9 - 16680690 Oct 12, 2018 (152)
48 The Danish reference pan genome NC_000019.9 - 16680690 Apr 27, 2020 (154)
49 gnomAD - Genomes NC_000019.10 - 16569879 Apr 27, 2021 (155)
50 Genome of the Netherlands Release 5 NC_000019.9 - 16680690 Apr 27, 2020 (154)
51 KOREAN population from KRGDB NC_000019.9 - 16680690 Apr 27, 2020 (154)
52 Korean Genome Project NC_000019.10 - 16569879 Apr 27, 2020 (154)
53 Northern Sweden NC_000019.9 - 16680690 Jul 13, 2019 (153)
54 Qatari NC_000019.9 - 16680690 Apr 27, 2020 (154)
55 SGDP_PRJ NC_000019.9 - 16680690 Apr 27, 2020 (154)
56 Siberian NC_000019.9 - 16680690 Apr 27, 2020 (154)
57 8.3KJPN NC_000019.9 - 16680690 Apr 27, 2021 (155)
58 14KJPN NC_000019.10 - 16569879 Oct 13, 2022 (156)
59 TopMed NC_000019.10 - 16569879 Apr 27, 2021 (155)
60 UK 10K study - Twins NC_000019.9 - 16680690 Oct 12, 2018 (152)
61 A Vietnamese Genetic Variation Database NC_000019.9 - 16680690 Jul 13, 2019 (153)
62 ALFA NC_000019.10 - 16569879 Apr 27, 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
ss1698194605 NC_000019.8:16541689:G:A NC_000019.10:16569878:G:A (self)
75920524, 42058987, 29742201, 4759294, 18737248, 45043227, 16182067, 19663629, 39886511, 10627431, 84952857, 42058987, 9295562, ss237617600, ss243836536, ss565882966, ss661739091, ss994135090, ss1081788947, ss1362535866, ss1428350164, ss1578574313, ss1637652070, ss1680646103, ss1937621707, ss2029583759, ss2158111077, ss2702716148, ss2961005955, ss3017181969, ss3352221070, ss3684003953, ss3742897202, ss3755867405, ss3835377507, ss3887869531, ss3937865833, ss5226983550, ss5433856499, ss5662072371, ss5840323321, ss5953490288 NC_000019.9:16680689:G:A NC_000019.10:16569878:G:A (self)
99663873, 535449903, 37332722, 119184715, 285068857, 12046609989, ss2224655885, ss3645511158, ss3702444556, ss3821121855, ss3980954721, ss5069523193, ss5306671370, ss5499276182, ss5612137938, ss5785347611, ss5817451061, ss5852223984, ss5927481658 NC_000019.10:16569878:G:A NC_000019.10:16569878:G:A (self)
12046609989 NC_000019.10:16569878:G:C NC_000019.10:16569878: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 rs77592861

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