Name: rs564289325
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.

rs564289325

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:88841852 (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 / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.000049 (13/264690, TOPMED)
A=0.000014 (2/138778, GnomAD)
A=0.000041 (5/120746, ExAC) (+ 6 more)
A=0.00004 (2/44782, ALFA)
A=0.0002 (1/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)
A=0.0010 (4/3854, ALSPAC)
A=0.0003 (1/3708, TWINSUK)
A=0.001 (1/998, GoNL)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ACAN : 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	44782	G=0.99996	A=0.00004
European	Sub	32776	G=0.99994	A=0.00006
African	Sub	3560	G=1.0000	A=0.0000
African Others	Sub	122	G=1.000	A=0.000
African American	Sub	3438	G=1.0000	A=0.0000
Asian	Sub	168	G=1.000	A=0.000
East Asian	Sub	112	G=1.000	A=0.000
Other Asian	Sub	56	G=1.00	A=0.00
Latin American 1	Sub	500	G=1.000	A=0.000
Latin American 2	Sub	628	G=1.000	A=0.000
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	7052	G=1.0000	A=0.0000

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=0.999951	A=0.000049
gnomAD - Genomes	Global	Study-wide	138778	G=0.999986	A=0.000014
gnomAD - Genomes	European	Sub	75436	G=0.99999	A=0.00001
gnomAD - Genomes	African	Sub	41446	G=0.99998	A=0.00002
gnomAD - Genomes	American	Sub	13328	G=1.00000	A=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3312	G=1.0000	A=0.0000
gnomAD - Genomes	East Asian	Sub	3126	G=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2130	G=1.0000	A=0.0000
ExAC	Global	Study-wide	120746	G=0.999959	A=0.000041
ExAC	Europe	Sub	73332	G=0.99995	A=0.00005
ExAC	Asian	Sub	25136	G=0.99996	A=0.00004
ExAC	American	Sub	11570	G=1.00000	A=0.00000
ExAC	African	Sub	9808	G=1.0000	A=0.0000
ExAC	Other	Sub	900	G=1.000	A=0.000
Allele Frequency Aggregator	Total	Global	44782	G=0.99996	A=0.00004
Allele Frequency Aggregator	European	Sub	32776	G=0.99994	A=0.00006
Allele Frequency Aggregator	Other	Sub	7052	G=1.0000	A=0.0000
Allele Frequency Aggregator	African	Sub	3560	G=1.0000	A=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	628	G=1.000	A=0.000
Allele Frequency Aggregator	Latin American 1	Sub	500	G=1.000	A=0.000
Allele Frequency Aggregator	Asian	Sub	168	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=0.9998	A=0.0002
1000Genomes_30x	African	Sub	1786	G=1.0000	A=0.0000
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=0.9991	A=0.0009
1000Genomes_30x	American	Sub	980	G=1.000	A=0.000
1000Genomes	Global	Study-wide	5008	G=0.9998	A=0.0002
1000Genomes	African	Sub	1322	G=1.0000	A=0.0000
1000Genomes	East Asian	Sub	1008	G=0.9990	A=0.0010
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=1.000	A=0.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9990	A=0.0010
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9997	A=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.999	A=0.001

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.88841852G>A
GRCh38.p14 chr 15	NC_000015.10:g.88841852G>T
GRCh37.p13 chr 15	NC_000015.9:g.89385083G>A
GRCh37.p13 chr 15	NC_000015.9:g.89385083G>T
ACAN RefSeqGene	NG_012794.1:g.43410G>A
ACAN RefSeqGene	NG_012794.1:g.43410G>T

Gene: ACAN, aggrecan (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ACAN transcript variant 3	NM_001369268.1:c.742G>A	A [GCC] > T [ACC]	Coding Sequence Variant
aggrecan core protein isoform 3 precursor	NP_001356197.1:p.Ala248Thr	A (Ala) > T (Thr)	Missense Variant
ACAN transcript variant 3	NM_001369268.1:c.742G>T	A [GCC] > S [TCC]	Coding Sequence Variant
aggrecan core protein isoform 3 precursor	NP_001356197.1:p.Ala248Ser	A (Ala) > S (Ser)	Missense Variant
ACAN transcript variant 2	NM_013227.4:c.742G>A	A [GCC] > T [ACC]	Coding Sequence Variant
aggrecan core protein isoform 2 precursor	NP_037359.3:p.Ala248Thr	A (Ala) > T (Thr)	Missense Variant
ACAN transcript variant 2	NM_013227.4:c.742G>T	A [GCC] > S [TCC]	Coding Sequence Variant
aggrecan core protein isoform 2 precursor	NP_037359.3:p.Ala248Ser	A (Ala) > S (Ser)	Missense Variant
ACAN transcript variant 1	NM_001135.4:c.742G>A	A [GCC] > T [ACC]	Coding Sequence Variant
aggrecan core protein isoform 1 precursor	NP_001126.3:p.Ala248Thr	A (Ala) > T (Thr)	Missense Variant
ACAN transcript variant 1	NM_001135.4:c.742G>T	A [GCC] > S [TCC]	Coding Sequence Variant
aggrecan core protein isoform 1 precursor	NP_001126.3:p.Ala248Ser	A (Ala) > S (Ser)	Missense Variant
ACAN transcript variant X1	XM_047432214.1:c.742G>A	A [GCC] > T [ACC]	Coding Sequence Variant
aggrecan core protein isoform X1	XP_047288170.1:p.Ala248Thr	A (Ala) > T (Thr)	Missense Variant
ACAN transcript variant X1	XM_047432214.1:c.742G>T	A [GCC] > S [TCC]	Coding Sequence Variant
aggrecan core protein isoform X1	XP_047288170.1:p.Ala248Ser	A (Ala) > S (Ser)	Missense Variant
ACAN transcript variant X2	XM_047432215.1:c.742G>A	A [GCC] > T [ACC]	Coding Sequence Variant
aggrecan core protein isoform X2	XP_047288171.1:p.Ala248Thr	A (Ala) > T (Thr)	Missense Variant
ACAN transcript variant X2	XM_047432215.1:c.742G>T	A [GCC] > S [TCC]	Coding Sequence Variant
aggrecan core protein isoform X2	XP_047288171.1:p.Ala248Ser	A (Ala) > S (Ser)	Missense Variant
ACAN transcript variant X3	XM_011521313.2:c.742G>A	A [GCC] > T [ACC]	Coding Sequence Variant
aggrecan core protein isoform X3	XP_011519615.1:p.Ala248Thr	A (Ala) > T (Thr)	Missense Variant
ACAN transcript variant X3	XM_011521313.2:c.742G>T	A [GCC] > S [TCC]	Coding Sequence Variant
aggrecan core protein isoform X3	XP_011519615.1:p.Ala248Ser	A (Ala) > S (Ser)	Missense Variant
ACAN transcript variant X3	XM_047432216.1:c.742G>A	A [GCC] > T [ACC]	Coding Sequence Variant
aggrecan core protein isoform X3	XP_047288172.1:p.Ala248Thr	A (Ala) > T (Thr)	Missense Variant
ACAN transcript variant X3	XM_047432216.1:c.742G>T	A [GCC] > S [TCC]	Coding Sequence Variant
aggrecan core protein isoform X3	XP_047288172.1:p.Ala248Ser	A (Ala) > S (Ser)	Missense Variant
ACAN transcript variant X4	XM_047432217.1:c.742G>A	A [GCC] > T [ACC]	Coding Sequence Variant
aggrecan core protein isoform X3	XP_047288173.1:p.Ala248Thr	A (Ala) > T (Thr)	Missense Variant
ACAN transcript variant X4	XM_047432217.1:c.742G>T	A [GCC] > S [TCC]	Coding Sequence Variant
aggrecan core protein isoform X3	XP_047288173.1:p.Ala248Ser	A (Ala) > S (Ser)	Missense Variant
ACAN transcript variant X6	XM_011521314.2:c.742G>A	A [GCC] > T [ACC]	Coding Sequence Variant
aggrecan core protein isoform X5	XP_011519616.1:p.Ala248Thr	A (Ala) > T (Thr)	Missense Variant
ACAN transcript variant X6	XM_011521314.2:c.742G>T	A [GCC] > S [TCC]	Coding Sequence Variant
aggrecan core protein isoform X5	XP_011519616.1:p.Ala248Ser	A (Ala) > S (Ser)	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	G=	A	T
GRCh38.p14 chr 15	NC_000015.10:g.88841852=	NC_000015.10:g.88841852G>A	NC_000015.10:g.88841852G>T
GRCh37.p13 chr 15	NC_000015.9:g.89385083=	NC_000015.9:g.89385083G>A	NC_000015.9:g.89385083G>T
ACAN RefSeqGene	NG_012794.1:g.43410=	NG_012794.1:g.43410G>A	NG_012794.1:g.43410G>T
ACAN transcript variant 2	NM_013227.4:c.742=	NM_013227.4:c.742G>A	NM_013227.4:c.742G>T
ACAN transcript variant 2	NM_013227.3:c.742=	NM_013227.3:c.742G>A	NM_013227.3:c.742G>T
ACAN transcript variant 1	NM_001135.4:c.742=	NM_001135.4:c.742G>A	NM_001135.4:c.742G>T
ACAN transcript variant 1	NM_001135.3:c.742=	NM_001135.3:c.742G>A	NM_001135.3:c.742G>T
ACAN transcript variant 3	NM_001369268.1:c.742=	NM_001369268.1:c.742G>A	NM_001369268.1:c.742G>T
ACAN transcript variant X3	XM_011521313.2:c.742=	XM_011521313.2:c.742G>A	XM_011521313.2:c.742G>T
ACAN transcript variant X6	XM_011521314.2:c.742=	XM_011521314.2:c.742G>A	XM_011521314.2:c.742G>T
ACAN transcript variant 5	NM_001411097.1:c.742=	NM_001411097.1:c.742G>A	NM_001411097.1:c.742G>T
ACAN transcript variant 4	NM_001411096.1:c.742=	NM_001411096.1:c.742G>A	NM_001411096.1:c.742G>T
ACAN transcript variant X3	XM_047432216.1:c.742=	XM_047432216.1:c.742G>A	XM_047432216.1:c.742G>T
ACAN transcript variant X1	XM_047432214.1:c.742=	XM_047432214.1:c.742G>A	XM_047432214.1:c.742G>T
ACAN transcript variant X2	XM_047432215.1:c.742=	XM_047432215.1:c.742G>A	XM_047432215.1:c.742G>T
ACAN transcript variant X4	XM_047432217.1:c.742=	XM_047432217.1:c.742G>A	XM_047432217.1:c.742G>T
aggrecan core protein isoform 2 precursor	NP_037359.3:p.Ala248=	NP_037359.3:p.Ala248Thr	NP_037359.3:p.Ala248Ser
aggrecan core protein isoform 1 precursor	NP_001126.3:p.Ala248=	NP_001126.3:p.Ala248Thr	NP_001126.3:p.Ala248Ser
aggrecan core protein isoform 3 precursor	NP_001356197.1:p.Ala248=	NP_001356197.1:p.Ala248Thr	NP_001356197.1:p.Ala248Ser
aggrecan core protein isoform X3	XP_011519615.1:p.Ala248=	XP_011519615.1:p.Ala248Thr	XP_011519615.1:p.Ala248Ser
aggrecan core protein isoform X5	XP_011519616.1:p.Ala248=	XP_011519616.1:p.Ala248Thr	XP_011519616.1:p.Ala248Ser
aggrecan core protein isoform X3	XP_047288172.1:p.Ala248=	XP_047288172.1:p.Ala248Thr	XP_047288172.1:p.Ala248Ser
aggrecan core protein isoform X1	XP_047288170.1:p.Ala248=	XP_047288170.1:p.Ala248Thr	XP_047288170.1:p.Ala248Ser
aggrecan core protein isoform X2	XP_047288171.1:p.Ala248=	XP_047288171.1:p.Ala248Thr	XP_047288171.1:p.Ala248Ser
aggrecan core protein isoform X3	XP_047288173.1:p.Ala248=	XP_047288173.1:p.Ala248Thr	XP_047288173.1:p.Ala248Ser

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#.

17 SubSNP, 11 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EVA-GONL	ss992060546	Aug 21, 2014 (142)
2	1000GENOMES	ss1354527901	Aug 21, 2014 (142)
3	EVA_UK10K_ALSPAC	ss1633567013	Apr 01, 2015 (144)
4	EVA_UK10K_TWINSUK	ss1676561046	Apr 01, 2015 (144)
5	EVA_EXAC	ss1691981554	Apr 01, 2015 (144)
6	HUMAN_LONGEVITY	ss2208932588	Dec 20, 2016 (150)
7	GNOMAD	ss2741487255	Nov 08, 2017 (151)
8	GNOMAD	ss2749378343	Nov 08, 2017 (151)
9	GNOMAD	ss2937962221	Nov 08, 2017 (151)
10	KHV_HUMAN_GENOMES	ss3818719296	Jul 13, 2019 (153)
11	TOPMED	ss5000743464	Apr 26, 2021 (155)
12	TRAN_CS_UWATERLOO	ss5314442035	Oct 16, 2022 (156)
13	EVA	ss5420949631	Oct 16, 2022 (156)
14	1000G_HIGH_COVERAGE	ss5601253538	Oct 16, 2022 (156)
15	EVA	ss5848410057	Oct 16, 2022 (156)
16	EVA	ss5876947386	Oct 16, 2022 (156)
17	EVA	ss5949458036	Oct 16, 2022 (156)
18	1000Genomes	NC_000015.9 - 89385083	Oct 12, 2018 (152)
19	1000Genomes_30x	NC_000015.10 - 88841852	Oct 16, 2022 (156)
20	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 89385083	Oct 12, 2018 (152)
21	ExAC	NC_000015.9 - 89385083	Oct 12, 2018 (152)
22	gnomAD - Genomes	NC_000015.10 - 88841852	Apr 26, 2021 (155)
23	gnomAD - Exomes Submission ignored due to conflicting rows: Row 10755372 (NC_000015.9:89385082:G:G 249076/249090, NC_000015.9:89385082:G:A 14/249090) Row 10755373 (NC_000015.9:89385082:G:G 249089/249090, NC_000015.9:89385082:G:T 1/249090)	-	Jul 13, 2019 (153)
24	gnomAD - Exomes Submission ignored due to conflicting rows: Row 10755372 (NC_000015.9:89385082:G:G 249076/249090, NC_000015.9:89385082:G:A 14/249090) Row 10755373 (NC_000015.9:89385082:G:G 249089/249090, NC_000015.9:89385082:G:T 1/249090)	-	Jul 13, 2019 (153)
25	Genome of the Netherlands Release 5	NC_000015.9 - 89385083	Apr 27, 2020 (154)
26	TopMed	NC_000015.10 - 88841852	Apr 26, 2021 (155)
27	UK 10K study - Twins	NC_000015.9 - 89385083	Oct 12, 2018 (152)
28	ALFA	NC_000015.10 - 88841852	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
67637365, 37562240, 2366592, 16760738, 37562240, ss992060546, ss1354527901, ss1633567013, ss1676561046, ss1691981554, ss2741487255, ss2749378343, ss2937962221, ss5420949631, ss5848410057, ss5949458036	NC_000015.9:89385082:G:A	NC_000015.10:88841851:G:A	(self)
88779473, 476872007, 216289124, 336700369, ss2208932588, ss3818719296, ss5000743464, ss5314442035, ss5601253538, ss5876947386	NC_000015.10:88841851:G:A	NC_000015.10:88841851:G:A	(self)
ss2741487255	NC_000015.9:89385082:G:T	NC_000015.10:88841851:G: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 rs564289325

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs564289325