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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.

rs3748932

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr2:100393544 (GRCh38.p13) 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=0.000008 (2/264690, TOPMED)
A=0.000012 (3/251344, GnomAD_exome)
T=0.000012 (3/242942, ALFA) (+ 5 more)
T=0.00011 (9/78702, PAGE_STUDY)
T=0.00286 (48/16760, 8.3KJPN)
T=0.0003 (1/2922, KOREAN)
T=0.0005 (1/1832, Korea1K)
T=0.000 (0/404, HapMap)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CHST10 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 2 NC_000002.12:g.100393544C>A
GRCh38.p13 chr 2 NC_000002.12:g.100393544C>T
GRCh37.p13 chr 2 NC_000002.11:g.101010006C>A
GRCh37.p13 chr 2 NC_000002.11:g.101010006C>T
CHST10 RefSeqGene NG_028153.1:g.29125G>T
CHST10 RefSeqGene NG_028153.1:g.29125G>A
Gene: CHST10, carbohydrate sulfotransferase 10 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CHST10 transcript NM_004854.5:c.772G>T D [GAC] > Y [TAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 precursor NP_004845.1:p.Asp258Tyr D (Asp) > Y (Tyr) Missense Variant
CHST10 transcript NM_004854.5:c.772G>A D [GAC] > N [AAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 precursor NP_004845.1:p.Asp258Asn D (Asp) > N (Asn) Missense Variant
CHST10 transcript variant X2 XM_011512208.1:c.772G>T D [GAC] > Y [TAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_011510510.1:p.Asp258Tyr D (Asp) > Y (Tyr) Missense Variant
CHST10 transcript variant X2 XM_011512208.1:c.772G>A D [GAC] > N [AAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_011510510.1:p.Asp258Asn D (Asp) > N (Asn) Missense Variant
CHST10 transcript variant X4 XM_011512210.1:c.772G>T D [GAC] > Y [TAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_011510512.1:p.Asp258Tyr D (Asp) > Y (Tyr) Missense Variant
CHST10 transcript variant X4 XM_011512210.1:c.772G>A D [GAC] > N [AAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_011510512.1:p.Asp258Asn D (Asp) > N (Asn) Missense Variant
CHST10 transcript variant X7 XM_011512211.1:c.772G>T D [GAC] > Y [TAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_011510513.1:p.Asp258Tyr D (Asp) > Y (Tyr) Missense Variant
CHST10 transcript variant X7 XM_011512211.1:c.772G>A D [GAC] > N [AAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_011510513.1:p.Asp258Asn D (Asp) > N (Asn) Missense Variant
CHST10 transcript variant X1 XM_011512207.2:c.772G>T D [GAC] > Y [TAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_011510509.1:p.Asp258Tyr D (Asp) > Y (Tyr) Missense Variant
CHST10 transcript variant X1 XM_011512207.2:c.772G>A D [GAC] > N [AAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_011510509.1:p.Asp258Asn D (Asp) > N (Asn) Missense Variant
CHST10 transcript variant X3 XM_024453248.1:c.772G>T D [GAC] > Y [TAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_024309016.1:p.Asp258Tyr D (Asp) > Y (Tyr) Missense Variant
CHST10 transcript variant X3 XM_024453248.1:c.772G>A D [GAC] > N [AAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_024309016.1:p.Asp258Asn D (Asp) > N (Asn) Missense Variant
CHST10 transcript variant X5 XM_017005380.2:c.772G>T D [GAC] > Y [TAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_016860869.1:p.Asp258Tyr D (Asp) > Y (Tyr) Missense Variant
CHST10 transcript variant X5 XM_017005380.2:c.772G>A D [GAC] > N [AAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_016860869.1:p.Asp258Asn D (Asp) > N (Asn) Missense Variant
CHST10 transcript variant X6 XM_017005381.2:c.772G>T D [GAC] > Y [TAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_016860870.1:p.Asp258Tyr D (Asp) > Y (Tyr) Missense Variant
CHST10 transcript variant X6 XM_017005381.2:c.772G>A D [GAC] > N [AAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_016860870.1:p.Asp258Asn D (Asp) > N (Asn) Missense Variant
CHST10 transcript variant X8 XM_017005382.2:c.772G>T D [GAC] > Y [TAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_016860871.1:p.Asp258Tyr D (Asp) > Y (Tyr) Missense Variant
CHST10 transcript variant X8 XM_017005382.2:c.772G>A D [GAC] > N [AAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_016860871.1:p.Asp258Asn D (Asp) > N (Asn) Missense Variant
CHST10 transcript variant X9 XM_017005383.2:c.772G>T D [GAC] > Y [TAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_016860872.1:p.Asp258Tyr D (Asp) > Y (Tyr) Missense Variant
CHST10 transcript variant X9 XM_017005383.2:c.772G>A D [GAC] > N [AAC] Coding Sequence Variant
carbohydrate sulfotransferase 10 isoform X1 XP_016860872.1:p.Asp258Asn D (Asp) > N (Asn) Missense 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 242942 C=0.999984 A=0.000004, T=0.000012
European Sub 214204 C=0.999995 A=0.000005, T=0.000000
African Sub 8326 C=0.9999 A=0.0000, T=0.0001
African Others Sub 320 C=1.000 A=0.000, T=0.000
African American Sub 8006 C=0.9999 A=0.0000, T=0.0001
Asian Sub 3930 C=0.9995 A=0.0000, T=0.0005
East Asian Sub 3158 C=0.9994 A=0.0000, T=0.0006
Other Asian Sub 772 C=1.000 A=0.000, T=0.000
Latin American 1 Sub 1040 C=1.0000 A=0.0000, T=0.0000
Latin American 2 Sub 3028 C=1.0000 A=0.0000, T=0.0000
South Asian Sub 5204 C=1.0000 A=0.0000, T=0.0000
Other Sub 7210 C=1.0000 A=0.0000, T=0.0000


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=0.999992 A=0.000008
gnomAD - Exomes Global Study-wide 251344 C=0.999988 A=0.000012
gnomAD - Exomes European Sub 135294 C=0.999978 A=0.000022
gnomAD - Exomes Asian Sub 49006 C=1.00000 A=0.00000
gnomAD - Exomes American Sub 34592 C=1.00000 A=0.00000
gnomAD - Exomes African Sub 16242 C=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 C=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6134 C=1.0000 A=0.0000
The PAGE Study Global Study-wide 78702 C=0.99989 T=0.00011
The PAGE Study AfricanAmerican Sub 32516 C=1.00000 T=0.00000
The PAGE Study Mexican Sub 10810 C=1.00000 T=0.00000
The PAGE Study Asian Sub 8318 C=0.9989 T=0.0011
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
8.3KJPN JAPANESE Study-wide 16760 C=0.99714 T=0.00286
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9997 T=0.0003
Korean Genome Project KOREAN Study-wide 1832 C=0.9995 T=0.0005
HapMap Global Study-wide 404 C=1.000 T=0.000
HapMap Asian Sub 168 C=1.000 T=0.000
HapMap African Sub 118 C=1.000 T=0.000
HapMap American Sub 118 C=1.000 T=0.000
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.p13 chr 2 NC_000002.12:g.100393544= NC_000002.12:g.100393544C>A NC_000002.12:g.100393544C>T
GRCh37.p13 chr 2 NC_000002.11:g.101010006= NC_000002.11:g.101010006C>A NC_000002.11:g.101010006C>T
CHST10 RefSeqGene NG_028153.1:g.29125= NG_028153.1:g.29125G>T NG_028153.1:g.29125G>A
CHST10 transcript NM_004854.5:c.772= NM_004854.5:c.772G>T NM_004854.5:c.772G>A
CHST10 transcript NM_004854.4:c.772= NM_004854.4:c.772G>T NM_004854.4:c.772G>A
CHST10 transcript variant X5 XM_017005380.2:c.772= XM_017005380.2:c.772G>T XM_017005380.2:c.772G>A
CHST10 transcript variant X8 XM_017005382.2:c.772= XM_017005382.2:c.772G>T XM_017005382.2:c.772G>A
CHST10 transcript variant X9 XM_017005383.2:c.772= XM_017005383.2:c.772G>T XM_017005383.2:c.772G>A
CHST10 transcript variant X6 XM_017005381.2:c.772= XM_017005381.2:c.772G>T XM_017005381.2:c.772G>A
CHST10 transcript variant X1 XM_011512207.2:c.772= XM_011512207.2:c.772G>T XM_011512207.2:c.772G>A
CHST10 transcript variant X4 XM_011512210.1:c.772= XM_011512210.1:c.772G>T XM_011512210.1:c.772G>A
CHST10 transcript variant X2 XM_011512208.1:c.772= XM_011512208.1:c.772G>T XM_011512208.1:c.772G>A
CHST10 transcript variant X3 XM_024453248.1:c.772= XM_024453248.1:c.772G>T XM_024453248.1:c.772G>A
CHST10 transcript variant X7 XM_011512211.1:c.772= XM_011512211.1:c.772G>T XM_011512211.1:c.772G>A
carbohydrate sulfotransferase 10 precursor NP_004845.1:p.Asp258= NP_004845.1:p.Asp258Tyr NP_004845.1:p.Asp258Asn
carbohydrate sulfotransferase 10 isoform X1 XP_016860869.1:p.Asp258= XP_016860869.1:p.Asp258Tyr XP_016860869.1:p.Asp258Asn
carbohydrate sulfotransferase 10 isoform X1 XP_016860871.1:p.Asp258= XP_016860871.1:p.Asp258Tyr XP_016860871.1:p.Asp258Asn
carbohydrate sulfotransferase 10 isoform X1 XP_016860872.1:p.Asp258= XP_016860872.1:p.Asp258Tyr XP_016860872.1:p.Asp258Asn
carbohydrate sulfotransferase 10 isoform X1 XP_016860870.1:p.Asp258= XP_016860870.1:p.Asp258Tyr XP_016860870.1:p.Asp258Asn
carbohydrate sulfotransferase 10 isoform X1 XP_011510509.1:p.Asp258= XP_011510509.1:p.Asp258Tyr XP_011510509.1:p.Asp258Asn
carbohydrate sulfotransferase 10 isoform X1 XP_011510512.1:p.Asp258= XP_011510512.1:p.Asp258Tyr XP_011510512.1:p.Asp258Asn
carbohydrate sulfotransferase 10 isoform X1 XP_011510510.1:p.Asp258= XP_011510510.1:p.Asp258Tyr XP_011510510.1:p.Asp258Asn
carbohydrate sulfotransferase 10 isoform X1 XP_024309016.1:p.Asp258= XP_024309016.1:p.Asp258Tyr XP_024309016.1:p.Asp258Asn
carbohydrate sulfotransferase 10 isoform X1 XP_011510513.1:p.Asp258= XP_011510513.1:p.Asp258Tyr XP_011510513.1:p.Asp258Asn
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#.

55 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4934955 Aug 28, 2002 (107)
2 PERLEGEN ss68822533 May 17, 2007 (127)
3 ILLUMINA ss74855139 Dec 07, 2007 (129)
4 ILLUMINA ss154265144 Dec 01, 2009 (131)
5 ILLUMINA ss159441974 Dec 01, 2009 (131)
6 ILLUMINA ss160635976 Dec 01, 2009 (131)
7 ILLUMINA ss173622443 Jul 04, 2010 (132)
8 ILLUMINA ss480814036 May 04, 2012 (137)
9 ILLUMINA ss480829675 May 04, 2012 (137)
10 ILLUMINA ss481758693 Sep 08, 2015 (146)
11 ILLUMINA ss485201820 May 04, 2012 (137)
12 ILLUMINA ss537187915 Sep 08, 2015 (146)
13 ILLUMINA ss778894407 Sep 08, 2015 (146)
14 ILLUMINA ss783046902 Aug 21, 2014 (142)
15 ILLUMINA ss784005688 Sep 08, 2015 (146)
16 ILLUMINA ss832304696 Apr 01, 2015 (144)
17 ILLUMINA ss832953545 Aug 21, 2014 (142)
18 ILLUMINA ss833544374 Aug 21, 2014 (142)
19 ILLUMINA ss834355574 Sep 08, 2015 (146)
20 ILLUMINA ss1752301408 Sep 08, 2015 (146)
21 ILLUMINA ss1946047495 Feb 12, 2016 (147)
22 ILLUMINA ss1958442880 Feb 12, 2016 (147)
23 TOPMED ss2398824960 Dec 20, 2016 (150)
24 ILLUMINA ss2633648943 Nov 08, 2017 (151)
25 ILLUMINA ss2633648944 Nov 08, 2017 (151)
26 ILLUMINA ss2710907486 Nov 08, 2017 (151)
27 GNOMAD ss2732874744 Nov 08, 2017 (151)
28 AFFY ss2985180126 Nov 08, 2017 (151)
29 AFFY ss2985802148 Nov 08, 2017 (151)
30 ILLUMINA ss3021998067 Nov 08, 2017 (151)
31 TOPMED ss3317249250 Nov 08, 2017 (151)
32 ILLUMINA ss3625761807 Oct 11, 2018 (152)
33 ILLUMINA ss3628123889 Oct 11, 2018 (152)
34 ILLUMINA ss3631613842 Oct 11, 2018 (152)
35 ILLUMINA ss3633209711 Oct 11, 2018 (152)
36 ILLUMINA ss3633921836 Oct 11, 2018 (152)
37 ILLUMINA ss3634779090 Oct 11, 2018 (152)
38 ILLUMINA ss3635607883 Oct 11, 2018 (152)
39 ILLUMINA ss3636466456 Oct 11, 2018 (152)
40 ILLUMINA ss3637359794 Oct 11, 2018 (152)
41 ILLUMINA ss3638276069 Oct 11, 2018 (152)
42 ILLUMINA ss3640486392 Oct 11, 2018 (152)
43 ILLUMINA ss3643244780 Oct 11, 2018 (152)
44 ILLUMINA ss3644750239 Oct 11, 2018 (152)
45 ILLUMINA ss3652434983 Oct 11, 2018 (152)
46 ILLUMINA ss3653946718 Oct 11, 2018 (152)
47 ILLUMINA ss3725808078 Jul 13, 2019 (153)
48 ILLUMINA ss3744179719 Jul 13, 2019 (153)
49 ILLUMINA ss3745078981 Jul 13, 2019 (153)
50 PAGE_CC ss3770937197 Jul 13, 2019 (153)
51 ILLUMINA ss3772575716 Jul 13, 2019 (153)
52 KRGDB ss3898467783 Apr 25, 2020 (154)
53 KOGIC ss3948526860 Apr 25, 2020 (154)
54 TOPMED ss4516523504 Apr 26, 2021 (155)
55 TOMMO_GENOMICS ss5152855574 Apr 26, 2021 (155)
56 gnomAD - Exomes NC_000002.11 - 101010006 Jul 13, 2019 (153)
57 HapMap NC_000002.12 - 100393544 Apr 25, 2020 (154)
58 KOREAN population from KRGDB NC_000002.11 - 101010006 Apr 25, 2020 (154)
59 Korean Genome Project NC_000002.12 - 100393544 Apr 25, 2020 (154)
60 The PAGE Study NC_000002.12 - 100393544 Jul 13, 2019 (153)
61 8.3KJPN NC_000002.11 - 101010006 Apr 26, 2021 (155)
62 TopMed NC_000002.12 - 100393544 Apr 26, 2021 (155)
63 ALFA NC_000002.12 - 100393544 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
1930513, ss2398824960, ss2732874744 NC_000002.11:101010005:C:A NC_000002.12:100393543:C:A (self)
199854754, 320346383, 8593275010, ss3317249250, ss4516523504 NC_000002.12:100393543:C:A NC_000002.12:100393543:C:A (self)
ss480814036, ss3643244780 NC_000002.10:100376437:C:T NC_000002.12:100393543:C:T (self)
5645177, 10824881, ss480829675, ss481758693, ss485201820, ss537187915, ss778894407, ss783046902, ss784005688, ss832304696, ss832953545, ss833544374, ss834355574, ss1752301408, ss1946047495, ss1958442880, ss2633648943, ss2633648944, ss2710907486, ss2985180126, ss2985802148, ss3021998067, ss3625761807, ss3628123889, ss3631613842, ss3633209711, ss3633921836, ss3634779090, ss3635607883, ss3636466456, ss3637359794, ss3638276069, ss3640486392, ss3644750239, ss3652434983, ss3653946718, ss3744179719, ss3745078981, ss3772575716, ss3898467783, ss5152855574 NC_000002.11:101010005:C:T NC_000002.12:100393543:C:T (self)
1853229, 4904861, 158666, 8593275010, ss3725808078, ss3770937197, ss3948526860 NC_000002.12:100393543:C:T NC_000002.12:100393543:C:T (self)
ss4934955, ss68822533, ss74855139, ss154265144, ss159441974, ss160635976, ss173622443 NT_022171.15:5683834:C:T NC_000002.12:100393543: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 rs3748932

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.post596+ae089ad