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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.

rs779115203

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:72008333 (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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
A=0.000022 (4/182772, GnomAD_exome)
A=0.00000 (0/14050, ALFA) (+ 2 more)
T=0.0000 (0/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CHST3 : Missense 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 14050 C=1.00000 A=0.00000
European Sub 9690 C=1.0000 A=0.0000
African Sub 2898 C=1.0000 A=0.0000
African Others Sub 114 C=1.000 A=0.000
African American Sub 2784 C=1.0000 A=0.0000
Asian Sub 112 C=1.000 A=0.000
East Asian Sub 86 C=1.00 A=0.00
Other Asian Sub 26 C=1.00 A=0.00
Latin American 1 Sub 146 C=1.000 A=0.000
Latin American 2 Sub 610 C=1.000 A=0.000
South Asian Sub 98 C=1.00 A=0.00
Other Sub 496 C=1.000 A=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=0.999996 A=0.000004
gnomAD - Exomes Global Study-wide 182772 C=0.999978 A=0.000022
gnomAD - Exomes European Sub 93088 C=1.00000 A=0.00000
gnomAD - Exomes Asian Sub 37948 C=0.99989 A=0.00011
gnomAD - Exomes American Sub 27514 C=1.00000 A=0.00000
gnomAD - Exomes African Sub 10580 C=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 8752 C=1.0000 A=0.0000
gnomAD - Exomes Other Sub 4890 C=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 14050 C=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9690 C=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 C=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 C=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=1.0000 T=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9997 T=0.0003
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.72008333C>A
GRCh38.p14 chr 10 NC_000010.11:g.72008333C>T
GRCh37.p13 chr 10 NC_000010.10:g.73768091C>A
GRCh37.p13 chr 10 NC_000010.10:g.73768091C>T
CHST3 RefSeqGene NG_012635.1:g.48972C>A
CHST3 RefSeqGene NG_012635.1:g.48972C>T
Gene: CHST3, carbohydrate sulfotransferase 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHST3 transcript NM_004273.5:c.1302C>A F [TTC] > L [TTA] Coding Sequence Variant
carbohydrate sulfotransferase 3 NP_004264.2:p.Phe434Leu F (Phe) > L (Leu) Missense Variant
CHST3 transcript NM_004273.5:c.1302C>T F [TTC] > F [TTT] Coding Sequence Variant
carbohydrate sulfotransferase 3 NP_004264.2:p.Phe434= F (Phe) > F (Phe) Synonymous Variant
CHST3 transcript variant X1 XM_006718075.5:c.1302C>A F [TTC] > L [TTA] Coding Sequence Variant
carbohydrate sulfotransferase 3 isoform X1 XP_006718138.1:p.Phe434Leu F (Phe) > L (Leu) Missense Variant
CHST3 transcript variant X1 XM_006718075.5:c.1302C>T F [TTC] > F [TTT] Coding Sequence Variant
carbohydrate sulfotransferase 3 isoform X1 XP_006718138.1:p.Phe434= F (Phe) > F (Phe) Synonymous Variant
CHST3 transcript variant X2 XM_011540369.3:c.1302C>A F [TTC] > L [TTA] Coding Sequence Variant
carbohydrate sulfotransferase 3 isoform X1 XP_011538671.1:p.Phe434Leu F (Phe) > L (Leu) Missense Variant
CHST3 transcript variant X2 XM_011540369.3:c.1302C>T F [TTC] > F [TTT] Coding Sequence Variant
carbohydrate sulfotransferase 3 isoform X1 XP_011538671.1:p.Phe434= F (Phe) > F (Phe) Synonymous Variant
CHST3 transcript variant X3 XM_047426022.1:c.1302C>A F [TTC] > L [TTA] Coding Sequence Variant
carbohydrate sulfotransferase 3 isoform X1 XP_047281978.1:p.Phe434Leu F (Phe) > L (Leu) Missense Variant
CHST3 transcript variant X3 XM_047426022.1:c.1302C>T F [TTC] > F [TTT] Coding Sequence Variant
carbohydrate sulfotransferase 3 isoform X1 XP_047281978.1:p.Phe434= F (Phe) > F (Phe) Synonymous 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= A T
GRCh38.p14 chr 10 NC_000010.11:g.72008333= NC_000010.11:g.72008333C>A NC_000010.11:g.72008333C>T
GRCh37.p13 chr 10 NC_000010.10:g.73768091= NC_000010.10:g.73768091C>A NC_000010.10:g.73768091C>T
CHST3 RefSeqGene NG_012635.1:g.48972= NG_012635.1:g.48972C>A NG_012635.1:g.48972C>T
CHST3 transcript NM_004273.5:c.1302= NM_004273.5:c.1302C>A NM_004273.5:c.1302C>T
CHST3 transcript NM_004273.4:c.1302= NM_004273.4:c.1302C>A NM_004273.4:c.1302C>T
CHST3 transcript variant X1 XM_006718075.5:c.1302= XM_006718075.5:c.1302C>A XM_006718075.5:c.1302C>T
CHST3 transcript variant X2 XM_006718075.4:c.1302= XM_006718075.4:c.1302C>A XM_006718075.4:c.1302C>T
CHST3 transcript variant X2 XM_006718075.3:c.1302= XM_006718075.3:c.1302C>A XM_006718075.3:c.1302C>T
CHST3 transcript variant X2 XM_006718075.2:c.1302= XM_006718075.2:c.1302C>A XM_006718075.2:c.1302C>T
CHST3 transcript variant X1 XM_006718075.1:c.1302= XM_006718075.1:c.1302C>A XM_006718075.1:c.1302C>T
CHST3 transcript variant X2 XM_011540369.3:c.1302= XM_011540369.3:c.1302C>A XM_011540369.3:c.1302C>T
CHST3 transcript variant X1 XM_011540369.2:c.1302= XM_011540369.2:c.1302C>A XM_011540369.2:c.1302C>T
CHST3 transcript variant X1 XM_011540369.1:c.1302= XM_011540369.1:c.1302C>A XM_011540369.1:c.1302C>T
CHST3 transcript variant X3 XM_047426022.1:c.1302= XM_047426022.1:c.1302C>A XM_047426022.1:c.1302C>T
carbohydrate sulfotransferase 3 NP_004264.2:p.Phe434= NP_004264.2:p.Phe434Leu NP_004264.2:p.Phe434=
carbohydrate sulfotransferase 3 isoform X1 XP_006718138.1:p.Phe434= XP_006718138.1:p.Phe434Leu XP_006718138.1:p.Phe434=
carbohydrate sulfotransferase 3 isoform X1 XP_011538671.1:p.Phe434= XP_011538671.1:p.Phe434Leu XP_011538671.1:p.Phe434=
carbohydrate sulfotransferase 3 isoform X1 XP_047281978.1:p.Phe434= XP_047281978.1:p.Phe434Leu XP_047281978.1:p.Phe434=
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#.

7 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_UK10K_ALSPAC ss1624862568 Apr 01, 2015 (144)
2 EVA_UK10K_TWINSUK ss1667856601 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2175888419 Dec 20, 2016 (150)
4 GNOMAD ss2738318961 Nov 08, 2017 (151)
5 GNOMAD ss2748411029 Nov 08, 2017 (151)
6 VINODS ss4028259552 Apr 26, 2021 (155)
7 TOPMED ss4857158299 Apr 26, 2021 (155)
8 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 73768091 Oct 12, 2018 (152)
9 gnomAD - Exomes NC_000010.10 - 73768091 Jul 13, 2019 (153)
10 TopMed NC_000010.11 - 72008333 Apr 26, 2021 (155)
11 UK 10K study - Twins NC_000010.10 - 73768091 Oct 12, 2018 (152)
12 ALFA NC_000010.11 - 72008333 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
7516968, ss2738318961, ss2748411029 NC_000010.10:73768090:C:A NC_000010.11:72008332:C:A (self)
72703954, 8225018138, ss4857158299 NC_000010.11:72008332:C:A NC_000010.11:72008332:C:A (self)
27979301, 27979301, ss1624862568, ss1667856601 NC_000010.10:73768090:C:T NC_000010.11:72008332:C:T (self)
ss2175888419, ss4028259552 NC_000010.11:72008332:C:T NC_000010.11:72008332: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 rs779115203

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