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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.

rs60924680

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:72009841 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.041626 (11018/264690, TOPMED)
A=0.039438 (5529/140194, GnomAD)
A=0.00004 (1/28258, 14KJPN) (+ 5 more)
A=0.02691 (388/14420, ALFA)
A=0.0450 (288/6404, 1000G_30x)
A=0.0429 (215/5008, 1000G)
A=0.019 (4/216, Qatari)
G=0.46 (12/26, SGDP_PRJ)
Clinical Significance
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 G=0.97309 A=0.02691
European Sub 9824 G=0.9994 A=0.0006
African Sub 2946 G=0.8842 A=0.1158
African Others Sub 114 G=0.904 A=0.096
African American Sub 2832 G=0.8835 A=0.1165
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.932 A=0.068
Latin American 2 Sub 610 G=0.995 A=0.005
South Asian Sub 98 G=1.00 A=0.00
Other Sub 684 G=0.959 A=0.041


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=0.958374 A=0.041626
gnomAD - Genomes Global Study-wide 140194 G=0.960562 A=0.039438
gnomAD - Genomes European Sub 75940 G=0.99954 A=0.00046
gnomAD - Genomes African Sub 41992 G=0.87469 A=0.12531
gnomAD - Genomes American Sub 13656 G=0.98806 A=0.01194
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2148 G=0.9679 A=0.0321
14KJPN JAPANESE Study-wide 28258 G=0.99996 A=0.00004
Allele Frequency Aggregator Total Global 14420 G=0.97309 A=0.02691
Allele Frequency Aggregator European Sub 9824 G=0.9994 A=0.0006
Allele Frequency Aggregator African Sub 2946 G=0.8842 A=0.1158
Allele Frequency Aggregator Other Sub 684 G=0.959 A=0.041
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.995 A=0.005
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.932 A=0.068
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9550 A=0.0450
1000Genomes_30x African Sub 1786 G=0.8455 A=0.1545
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.988 A=0.012
1000Genomes Global Study-wide 5008 G=0.9571 A=0.0429
1000Genomes African Sub 1322 G=0.8434 A=0.1566
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.988 A=0.012
Qatari Global Study-wide 216 G=0.981 A=0.019
SGDP_PRJ Global Study-wide 26 G=0.46 A=0.54
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.72009841G>A
GRCh37.p13 chr 10 NC_000010.10:g.73769599G>A
CHST3 RefSeqGene NG_012635.1:g.50480G>A
Gene: CHST3, carbohydrate sulfotransferase 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHST3 transcript NM_004273.5:c.*1370= N/A 3 Prime UTR Variant
CHST3 transcript variant X1 XM_006718075.5:c.*1370= N/A 3 Prime UTR Variant
CHST3 transcript variant X2 XM_011540369.3:c.*1370= N/A 3 Prime UTR Variant
CHST3 transcript variant X3 XM_047426022.1:c.*1370= 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.

Allele: A (allele ID: 322815 )
ClinVar Accession Disease Names Clinical Significance
RCV000263787.3 Spondyloepiphyseal dysplasia congenita Likely-Benign
RCV000300323.3 Spondyloepiphyseal dysplasia with congenital joint dislocations Likely-Benign
RCV000354014.3 Skeletal dysplasia Likely-Benign
RCV000369039.3 Larsen syndrome Likely-Benign
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
GRCh38.p14 chr 10 NC_000010.11:g.72009841= NC_000010.11:g.72009841G>A
GRCh37.p13 chr 10 NC_000010.10:g.73769599= NC_000010.10:g.73769599G>A
CHST3 RefSeqGene NG_012635.1:g.50480= NG_012635.1:g.50480G>A
CHST3 transcript NM_004273.5:c.*1370= NM_004273.5:c.*1370G>A
CHST3 transcript NM_004273.4:c.*1370= NM_004273.4:c.*1370G>A
CHST3 transcript variant X1 XM_006718075.5:c.*1370= XM_006718075.5:c.*1370G>A
CHST3 transcript variant X2 XM_006718075.4:c.*1370= XM_006718075.4:c.*1370G>A
CHST3 transcript variant X2 XM_006718075.3:c.*1370= XM_006718075.3:c.*1370G>A
CHST3 transcript variant X2 XM_006718075.2:c.*1370= XM_006718075.2:c.*1370G>A
CHST3 transcript variant X1 XM_006718075.1:c.*1370= XM_006718075.1:c.*1370G>A
CHST3 transcript variant X2 XM_011540369.3:c.*1370= XM_011540369.3:c.*1370G>A
CHST3 transcript variant X1 XM_011540369.2:c.*1370= XM_011540369.2:c.*1370G>A
CHST3 transcript variant X1 XM_011540369.1:c.*1370= XM_011540369.1:c.*1370G>A
CHST3 transcript variant X3 XM_047426022.1:c.*1370= XM_047426022.1:c.*1370G>A
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#.

22 SubSNP, 8 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HGSV ss86086591 Dec 15, 2007 (129)
2 BUSHMAN ss201698008 Jul 04, 2010 (132)
3 1000GENOMES ss224803809 Jul 14, 2010 (132)
4 TISHKOFF ss562046094 Apr 25, 2013 (138)
5 1000GENOMES ss1337994664 Aug 21, 2014 (142)
6 EVA_DECODE ss1597310081 Apr 01, 2015 (144)
7 WEILL_CORNELL_DGM ss1931003963 Feb 12, 2016 (147)
8 HUMAN_LONGEVITY ss2175888538 Dec 20, 2016 (150)
9 GNOMAD ss2890334994 Nov 08, 2017 (151)
10 EVA_DECODE ss3690157067 Jul 13, 2019 (153)
11 KHV_HUMAN_GENOMES ss3813647503 Jul 13, 2019 (153)
12 SGDP_PRJ ss3874498975 Apr 26, 2020 (154)
13 TOPMED ss4857158741 Apr 26, 2021 (155)
14 1000G_HIGH_COVERAGE ss5284537524 Oct 16, 2022 (156)
15 EVA ss5394331834 Oct 16, 2022 (156)
16 HUGCELL_USP ss5480066551 Oct 16, 2022 (156)
17 1000G_HIGH_COVERAGE ss5578729260 Oct 16, 2022 (156)
18 SANFORD_IMAGENETICS ss5649570663 Oct 16, 2022 (156)
19 TOMMO_GENOMICS ss5744265128 Oct 16, 2022 (156)
20 EVA ss5824592482 Oct 16, 2022 (156)
21 EVA ss5879462004 Oct 16, 2022 (156)
22 EVA ss5940848090 Oct 16, 2022 (156)
23 1000Genomes NC_000010.10 - 73769599 Oct 12, 2018 (152)
24 1000Genomes_30x NC_000010.11 - 72009841 Oct 16, 2022 (156)
25 gnomAD - Genomes NC_000010.11 - 72009841 Apr 26, 2021 (155)
26 Qatari NC_000010.10 - 73769599 Apr 26, 2020 (154)
27 SGDP_PRJ NC_000010.10 - 73769599 Apr 26, 2020 (154)
28 14KJPN NC_000010.11 - 72009841 Oct 16, 2022 (156)
29 TopMed NC_000010.11 - 72009841 Apr 26, 2021 (155)
30 ALFA NC_000010.11 - 72009841 Apr 26, 2021 (155)
31 ClinVar RCV000263787.3 Oct 16, 2022 (156)
32 ClinVar RCV000300323.3 Oct 16, 2022 (156)
33 ClinVar RCV000354014.3 Oct 16, 2022 (156)
34 ClinVar RCV000369039.3 Oct 16, 2022 (156)
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
ss86086591 NC_000010.8:73439604:G:A NC_000010.11:72009840:G:A (self)
ss201698008, ss1597310081 NC_000010.9:73439604:G:A NC_000010.11:72009840:G:A (self)
50403167, 13045893, 26515955, ss224803809, ss562046094, ss1337994664, ss1931003963, ss2890334994, ss3874498975, ss5394331834, ss5649570663, ss5824592482, ss5940848090 NC_000010.10:73769598:G:A NC_000010.11:72009840:G:A (self)
RCV000263787.3, RCV000300323.3, RCV000354014.3, RCV000369039.3, 66255195, 356180532, 78102232, 72704396, 10112163533, ss2175888538, ss3690157067, ss3813647503, ss4857158741, ss5284537524, ss5480066551, ss5578729260, ss5744265128, ss5879462004 NC_000010.11:72009840:G:A NC_000010.11:72009840:G:A (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 rs60924680

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