Name: rs11247271
Published: September 21, 2022
License: Open Access

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.

rs11247271

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:101185517 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.00830 (190/22892, 14KJPN)
T=0.00650 (100/15394, 8.3KJPN)
G=0.00007 (1/14974, GnomAD) (+ 11 more)
T=0.47378 (5620/11862, ALFA)
T=0.4952 (1451/2930, KOREAN)
T=0.0308 (55/1786, Korea1K)
T=0.024 (24/998, GoNL)
T=0.023 (14/600, NorthernSweden)
C=0.500 (276/552, SGDP_PRJ)
T=0.500 (276/552, SGDP_PRJ)
C=0.500 (108/216, Qatari)
T=0.500 (108/216, Qatari)
C=0.50 (23/46, Siberian)
T=0.50 (23/46, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CHSY1 : 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	11862	C=0.52622	T=0.47378
European	Sub	7618	C=0.5234	T=0.4766
African	Sub	2816	C=0.5423	T=0.4577
African Others	Sub	108	C=0.519	T=0.481
African American	Sub	2708	C=0.5432	T=0.4568
Asian	Sub	108	C=0.509	T=0.491
East Asian	Sub	84	C=0.51	T=0.49
Other Asian	Sub	24	C=0.50	T=0.50
Latin American 1	Sub	146	C=0.514	T=0.486
Latin American 2	Sub	610	C=0.507	T=0.493
South Asian	Sub	94	C=0.51	T=0.49
Other	Sub	470	C=0.513	T=0.487

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
14KJPN	JAPANESE	Study-wide	22892	C=0.99170	T=0.00830
8.3KJPN	JAPANESE	Study-wide	15394	C=0.99350	T=0.00650
gnomAD - Genomes	Global	Study-wide	14974	C=0.99993	G=0.00007
gnomAD - Genomes	African	Sub	8684	C=0.9999	G=0.0001
gnomAD - Genomes	European	Sub	4754	C=1.0000	G=0.0000
gnomAD - Genomes	American	Sub	954	C=1.000	G=0.000
gnomAD - Genomes	Other	Sub	202	C=1.000	G=0.000
gnomAD - Genomes	East Asian	Sub	194	C=1.000	G=0.000
gnomAD - Genomes	Ashkenazi Jewish	Sub	186	C=1.000	G=0.000
Allele Frequency Aggregator	Total	Global	11862	C=0.52622	T=0.47378
Allele Frequency Aggregator	European	Sub	7618	C=0.5234	T=0.4766
Allele Frequency Aggregator	African	Sub	2816	C=0.5423	T=0.4577
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.507	T=0.493
Allele Frequency Aggregator	Other	Sub	470	C=0.513	T=0.487
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.514	T=0.486
Allele Frequency Aggregator	Asian	Sub	108	C=0.509	T=0.491
Allele Frequency Aggregator	South Asian	Sub	94	C=0.51	T=0.49
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.5048	T=0.4952
Korean Genome Project	KOREAN	Study-wide	1786	C=0.9692	T=0.0308
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.976	T=0.024
Northern Sweden	ACPOP	Study-wide	600	C=0.977	T=0.023
SGDP_PRJ	Global	Study-wide	552	C=0.500	T=0.500
Qatari	Global	Study-wide	216	C=0.500	T=0.500
Siberian	Global	Study-wide	46	C=0.50	T=0.50

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 15	NC_000015.10:g.101185517C>G
GRCh38.p14 chr 15	NC_000015.10:g.101185517C>T
GRCh37.p13 chr 15	NC_000015.9:g.101725722C>G
GRCh37.p13 chr 15	NC_000015.9:g.101725722C>T
CHSY1 RefSeqGene	NG_031908.1:g.71416G>C
CHSY1 RefSeqGene	NG_031908.1:g.71416G>A

Gene: CHSY1, chondroitin sulfate synthase 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CHSY1 transcript	NM_014918.5:c.817-6537G>C	N/A	Intron Variant
CHSY1 transcript variant X1	XM_011521364.3:c.901-6537… XM_011521364.3:c.901-6537G>C	N/A	Intron Variant
CHSY1 transcript variant X4	XM_017022011.2:c.-1+3911G… XM_017022011.2:c.-1+3911G>C	N/A	Intron Variant
CHSY1 transcript variant X3	XM_047432240.1:c.-1+2476G… XM_047432240.1:c.-1+2476G>C	N/A	Intron Variant
CHSY1 transcript variant X2	XM_024449873.1:c.38G>C	G [GGG] > A [GCG]	Coding Sequence Variant
chondroitin sulfate synthase 1 isoform X2	XP_024305641.1:p.Gly13Ala	G (Gly) > A (Ala)	Missense Variant
CHSY1 transcript variant X2	XM_024449873.1:c.38G>A	G [GGG] > E [GAG]	Coding Sequence Variant
chondroitin sulfate synthase 1 isoform X2	XP_024305641.1:p.Gly13Glu	G (Gly) > E (Glu)	Missense Variant

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

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=	G	T
GRCh38.p14 chr 15	NC_000015.10:g.101185517=	NC_000015.10:g.101185517C>G	NC_000015.10:g.101185517C>T
GRCh37.p13 chr 15	NC_000015.9:g.101725722=	NC_000015.9:g.101725722C>G	NC_000015.9:g.101725722C>T
CHSY1 RefSeqGene	NG_031908.1:g.71416=	NG_031908.1:g.71416G>C	NG_031908.1:g.71416G>A
CHSY1 transcript variant X2	XM_024449873.1:c.38=	XM_024449873.1:c.38G>C	XM_024449873.1:c.38G>A
chondroitin sulfate synthase 1 isoform X2	XP_024305641.1:p.Gly13=	XP_024305641.1:p.Gly13Ala	XP_024305641.1:p.Gly13Glu
CHSY1 transcript	NM_014918.4:c.817-6537=	NM_014918.4:c.817-6537G>C	NM_014918.4:c.817-6537G>A
CHSY1 transcript	NM_014918.5:c.817-6537=	NM_014918.5:c.817-6537G>C	NM_014918.5:c.817-6537G>A
CHSY1 transcript variant X1	XM_005254883.1:c.-1+2476=	XM_005254883.1:c.-1+2476G>C	XM_005254883.1:c.-1+2476G>A
CHSY1 transcript variant X1	XM_011521364.3:c.901-6537=	XM_011521364.3:c.901-6537G>C	XM_011521364.3:c.901-6537G>A
CHSY1 transcript variant X4	XM_017022011.2:c.-1+3911=	XM_017022011.2:c.-1+3911G>C	XM_017022011.2:c.-1+3911G>A
CHSY1 transcript variant X3	XM_047432240.1:c.-1+2476=	XM_047432240.1:c.-1+2476G>C	XM_047432240.1:c.-1+2476G>A

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#.

30 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss16678807	Feb 27, 2004 (120)
2	CSHL-HAPMAP	ss19321834	Feb 27, 2004 (120)
3	SSAHASNP	ss21228852	Apr 05, 2004 (121)
4	HGSV	ss77656870	Dec 07, 2007 (129)
5	HGSV	ss80321766	Dec 15, 2007 (130)
6	ENSEMBL	ss136533934	Dec 01, 2009 (131)
7	GMI	ss156956537	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss168605053	Jul 04, 2010 (132)
9	COMPLETE_GENOMICS	ss170478734	Jul 04, 2010 (132)
10	COMPLETE_GENOMICS	ss171636835	Jul 04, 2010 (132)
11	GMI	ss282396263	May 04, 2012 (137)
12	SSMP	ss660449561	Apr 25, 2013 (138)
13	EVA-GONL	ss992166682	Aug 21, 2014 (142)
14	WEILL_CORNELL_DGM	ss1935570316	Feb 12, 2016 (147)
15	JJLAB	ss2028572557	Sep 14, 2016 (149)
16	USC_VALOUEV	ss2156980381	Nov 08, 2017 (151)
17	GRF	ss2701472832	Nov 08, 2017 (151)
18	CSHL	ss3351281751	Nov 08, 2017 (151)
19	ACPOP	ss3741240195	Jul 13, 2019 (153)
20	SGDP_PRJ	ss3883690360	Apr 27, 2020 (154)
21	KRGDB	ss3932953964	Apr 27, 2020 (154)
22	KOGIC	ss3976891774	Apr 27, 2020 (154)
23	GNOMAD	ss4295081521	Apr 26, 2021 (155)
24	TOMMO_GENOMICS	ss5217889824	Apr 26, 2021 (155)
25	1000G_HIGH_COVERAGE	ss5299729311	Oct 16, 2022 (156)
26	SANFORD_IMAGENETICS	ss5658237933	Oct 16, 2022 (156)
27	TOMMO_GENOMICS	ss5772203240	Oct 16, 2022 (156)
28	YY_MCH	ss5815658157	Oct 16, 2022 (156)
29	EVA	ss5828700579	Oct 16, 2022 (156)
30	EVA	ss5851445100	Oct 16, 2022 (156)
31	gnomAD - Genomes	NC_000015.10 - 101185517	Apr 26, 2021 (155)
32	Genome of the Netherlands Release 5	NC_000015.9 - 101725722	Apr 27, 2020 (154)
33	KOREAN population from KRGDB	NC_000015.9 - 101725722	Apr 27, 2020 (154)
34	Korean Genome Project	NC_000015.10 - 101185517	Apr 27, 2020 (154)
35	Northern Sweden	NC_000015.9 - 101725722	Jul 13, 2019 (153)
36	Qatari	NC_000015.9 - 101725722	Apr 27, 2020 (154)
37	SGDP_PRJ	NC_000015.9 - 101725722	Apr 27, 2020 (154)
38	Siberian	NC_000015.9 - 101725722	Apr 27, 2020 (154)
39	8.3KJPN	NC_000015.9 - 101725722	Apr 26, 2021 (155)
40	14KJPN	NC_000015.10 - 101185517	Oct 16, 2022 (156)
41	ALFA	NC_000015.10 - 101185517	Apr 26, 2021 (155)

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).

Associated ID	History Updated (Build)
rs59835962	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
479630498, ss4295081521	NC_000015.10:101185516:C:G	NC_000015.10:101185516:C:G	(self)
ss77656870, ss80321766, ss168605053, ss170478734, ss171636835, ss282396263	NC_000015.8:99543244:C:T	NC_000015.10:101185516:C:T	(self)
16863647, 40131358, 14525060, 17612238, 35707340, 9496735, 75859131, ss660449561, ss992166682, ss1935570316, ss2028572557, ss2156980381, ss2701472832, ss3351281751, ss3741240195, ss3883690360, ss3932953964, ss5217889824, ss5658237933, ss5828700579	NC_000015.9:101725721:C:T	NC_000015.10:101185516:C:T	(self)
33269775, 106040344, 6062038368, ss3976891774, ss5299729311, ss5772203240, ss5815658157, ss5851445100	NC_000015.10:101185516:C:T	NC_000015.10:101185516:C:T	(self)
ss136533934, ss156956537	NT_010274.17:16691248:C:T	NC_000015.10:101185516:C:T	(self)
ss16678807, ss19321834, ss21228852	NT_035325.5:3167458:C:T	NC_000015.10:101185516:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs11247271

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs11247271