Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs767819169

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:72012770 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000151 (40/264690, TOPMED)
T=0.000128 (18/140248, GnomAD)
T=0.00021 (6/28258, 14KJPN) (+ 8 more)
T=0.00006 (1/16760, 8.3KJPN)
T=0.00014 (2/14420, ALFA)
T=0.0002 (1/6404, 1000G_30x)
T=0.0005 (2/3854, ALSPAC)
T=0.0008 (3/3708, TWINSUK)
T=0.005 (1/216, Vietnamese)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CHST3 : 3 Prime UTR 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 14420 C=0.99986 T=0.00014
European Sub 9824 C=0.9999 T=0.0001
African Sub 2946 C=0.9997 T=0.0003
African Others Sub 114 C=1.000 T=0.000
African American Sub 2832 C=0.9996 T=0.0004
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 684 C=1.000 T=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 C=0.999849 T=0.000151
gnomAD - Genomes Global Study-wide 140248 C=0.999872 T=0.000128
gnomAD - Genomes European Sub 75940 C=0.99980 T=0.00020
gnomAD - Genomes African Sub 42050 C=0.99993 T=0.00007
gnomAD - Genomes American Sub 13652 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3128 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
14KJPN JAPANESE Study-wide 28258 C=0.99979 T=0.00021
8.3KJPN JAPANESE Study-wide 16760 C=0.99994 T=0.00006
Allele Frequency Aggregator Total Global 14420 C=0.99986 T=0.00014
Allele Frequency Aggregator European Sub 9824 C=0.9999 T=0.0001
Allele Frequency Aggregator African Sub 2946 C=0.9997 T=0.0003
Allele Frequency Aggregator Other Sub 684 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9998 T=0.0002
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=0.9992 T=0.0008
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9995 T=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9992 T=0.0008
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.995 T=0.005
SGDP_PRJ Global Study-wide 2 C=0.5 T=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 10 NC_000010.11:g.72012770C>T
GRCh37.p13 chr 10 NC_000010.10:g.73772528C>T
CHST3 RefSeqGene NG_012635.1:g.53409C>T
Gene: CHST3, carbohydrate sulfotransferase 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHST3 transcript NM_004273.5:c.*4299= N/A 3 Prime UTR Variant
CHST3 transcript variant X1 XM_006718075.5:c.*4299= N/A 3 Prime UTR Variant
CHST3 transcript variant X2 XM_011540369.3:c.*4299= N/A 3 Prime UTR Variant
CHST3 transcript variant X3 XM_047426022.1:c.*4299= N/A 3 Prime UTR 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 C= T
GRCh38.p14 chr 10 NC_000010.11:g.72012770= NC_000010.11:g.72012770C>T
GRCh37.p13 chr 10 NC_000010.10:g.73772528= NC_000010.10:g.73772528C>T
CHST3 RefSeqGene NG_012635.1:g.53409= NG_012635.1:g.53409C>T
CHST3 transcript NM_004273.5:c.*4299= NM_004273.5:c.*4299C>T
CHST3 transcript NM_004273.4:c.*4299= NM_004273.4:c.*4299C>T
CHST3 transcript variant X1 XM_006718075.5:c.*4299= XM_006718075.5:c.*4299C>T
CHST3 transcript variant X2 XM_006718075.4:c.*4299= XM_006718075.4:c.*4299C>T
CHST3 transcript variant X2 XM_006718075.3:c.*4299= XM_006718075.3:c.*4299C>T
CHST3 transcript variant X2 XM_006718075.2:c.*4299= XM_006718075.2:c.*4299C>T
CHST3 transcript variant X1 XM_006718075.1:c.*4299= XM_006718075.1:c.*4299C>T
CHST3 transcript variant X2 XM_011540369.3:c.*4299= XM_011540369.3:c.*4299C>T
CHST3 transcript variant X1 XM_011540369.2:c.*4299= XM_011540369.2:c.*4299C>T
CHST3 transcript variant X1 XM_011540369.1:c.*4299= XM_011540369.1:c.*4299C>T
CHST3 transcript variant X3 XM_047426022.1:c.*4299= XM_047426022.1:c.*4299C>T
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#.

15 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_UK10K_ALSPAC ss1624862659 Apr 01, 2015 (144)
2 EVA_UK10K_TWINSUK ss1667856692 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2175888738 Dec 20, 2016 (150)
4 GNOMAD ss2890335227 Nov 08, 2017 (151)
5 EVA_DECODE ss3690157104 Jul 13, 2019 (153)
6 KHV_HUMAN_GENOMES ss3813647549 Jul 13, 2019 (153)
7 SGDP_PRJ ss3874499031 Apr 26, 2020 (154)
8 TOPMED ss4857159505 Apr 26, 2021 (155)
9 TOMMO_GENOMICS ss5198254717 Apr 26, 2021 (155)
10 EVA ss5394331985 Oct 16, 2022 (156)
11 HUGCELL_USP ss5480066631 Oct 16, 2022 (156)
12 1000G_HIGH_COVERAGE ss5578729387 Oct 16, 2022 (156)
13 TOMMO_GENOMICS ss5744265240 Oct 16, 2022 (156)
14 EVA ss5849630148 Oct 16, 2022 (156)
15 EVA ss5940848152 Oct 16, 2022 (156)
16 1000Genomes_30x NC_000010.11 - 72012770 Oct 16, 2022 (156)
17 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 73772528 Oct 12, 2018 (152)
18 gnomAD - Genomes NC_000010.11 - 72012770 Apr 26, 2021 (155)
19 SGDP_PRJ NC_000010.10 - 73772528 Apr 26, 2020 (154)
20 8.3KJPN NC_000010.10 - 73772528 Apr 26, 2021 (155)
21 14KJPN NC_000010.11 - 72012770 Oct 16, 2022 (156)
22 TopMed NC_000010.11 - 72012770 Apr 26, 2021 (155)
23 UK 10K study - Twins NC_000010.10 - 73772528 Oct 12, 2018 (152)
24 A Vietnamese Genetic Variation Database NC_000010.10 - 73772528 Jul 13, 2019 (153)
25 ALFA NC_000010.11 - 72012770 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
27979400, 26516011, 56224024, 27979400, 6215332, ss1624862659, ss1667856692, ss2890335227, ss3874499031, ss5198254717, ss5394331985, ss5940848152 NC_000010.10:73772527:C:T NC_000010.11:72012769:C:T (self)
66255322, 356181109, 78102344, 72705160, 2763345924, ss2175888738, ss3690157104, ss3813647549, ss4857159505, ss5480066631, ss5578729387, ss5744265240, ss5849630148 NC_000010.11:72012769:C:T NC_000010.11:72012769:C:T (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 rs767819169

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