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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.

rs190361551

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:88873918 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.002463 (652/264690, TOPMED)
T=0.002531 (630/248904, GnomAD_exome)
T=0.002617 (367/140246, GnomAD) (+ 10 more)
T=0.002756 (330/119758, ExAC)
T=0.00376 (177/47062, ALFA)
T=0.00382 (48/12564, GO-ESP)
T=0.0011 (7/6404, 1000G_30x)
T=0.0012 (6/5008, 1000G)
T=0.0020 (9/4480, Estonian)
T=0.0029 (11/3854, ALSPAC)
T=0.0030 (11/3708, TWINSUK)
T=0.004 (4/998, GoNL)
T=0.006 (3/534, MGP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ACAN : Synonymous 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 63424 C=0.99653 T=0.00347
European Sub 45256 C=0.99611 T=0.00389
African Sub 8316 C=0.9992 T=0.0008
African Others Sub 300 C=1.000 T=0.000
African American Sub 8016 C=0.9991 T=0.0009
Asian Sub 164 C=1.000 T=0.000
East Asian Sub 110 C=1.000 T=0.000
Other Asian Sub 54 C=1.00 T=0.00
Latin American 1 Sub 500 C=0.996 T=0.004
Latin American 2 Sub 626 C=1.000 T=0.000
South Asian Sub 94 C=1.00 T=0.00
Other Sub 8468 C=0.9959 T=0.0041


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=0.997537 T=0.002463
gnomAD - Exomes Global Study-wide 248904 C=0.997469 T=0.002531
gnomAD - Exomes European Sub 134254 C=0.996514 T=0.003486
gnomAD - Exomes Asian Sub 48578 C=0.99930 T=0.00070
gnomAD - Exomes American Sub 34510 C=0.99893 T=0.00107
gnomAD - Exomes African Sub 15456 C=0.99942 T=0.00058
gnomAD - Exomes Ashkenazi Jewish Sub 10056 C=0.99403 T=0.00597
gnomAD - Exomes Other Sub 6050 C=0.9964 T=0.0036
gnomAD - Genomes Global Study-wide 140246 C=0.997383 T=0.002617
gnomAD - Genomes European Sub 75956 C=0.99633 T=0.00367
gnomAD - Genomes African Sub 42032 C=0.99943 T=0.00057
gnomAD - Genomes American Sub 13654 C=0.99729 T=0.00271
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9931 T=0.0069
gnomAD - Genomes East Asian Sub 3130 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=0.9981 T=0.0019
ExAC Global Study-wide 119758 C=0.997244 T=0.002756
ExAC Europe Sub 72564 C=0.99592 T=0.00408
ExAC Asian Sub 25078 C=0.99944 T=0.00056
ExAC American Sub 11524 C=0.99905 T=0.00095
ExAC African Sub 9706 C=0.9994 T=0.0006
ExAC Other Sub 886 C=0.997 T=0.003
Allele Frequency Aggregator Total Global 47062 C=0.99624 T=0.00376
Allele Frequency Aggregator European Sub 35166 C=0.99602 T=0.00398
Allele Frequency Aggregator Other Sub 7034 C=0.9956 T=0.0044
Allele Frequency Aggregator African Sub 3478 C=0.9988 T=0.0012
Allele Frequency Aggregator Latin American 2 Sub 626 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 C=0.996 T=0.004
Allele Frequency Aggregator Asian Sub 164 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 12564 C=0.99618 T=0.00382
GO Exome Sequencing Project European American Sub 8404 C=0.9946 T=0.0054
GO Exome Sequencing Project African American Sub 4160 C=0.9993 T=0.0007
1000Genomes_30x Global Study-wide 6404 C=0.9989 T=0.0011
1000Genomes_30x African Sub 1786 C=0.9994 T=0.0006
1000Genomes_30x Europe Sub 1266 C=0.9968 T=0.0032
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=0.998 T=0.002
1000Genomes Global Study-wide 5008 C=0.9988 T=0.0012
1000Genomes African Sub 1322 C=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9970 T=0.0030
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.997 T=0.003
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9980 T=0.0020
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9971 T=0.0029
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9970 T=0.0030
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.996 T=0.004
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.994 T=0.006
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 15 NC_000015.10:g.88873918C>T
GRCh37.p13 chr 15 NC_000015.9:g.89417149C>T
ACAN RefSeqGene NG_012794.1:g.75476C>T
Gene: ACAN, aggrecan (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ACAN transcript variant 1 NM_001135.4:c.7220-487C>T N/A Intron Variant
ACAN transcript variant 3 NM_001369268.1:c.7524C>T S [TCC] > S [TCT] Coding Sequence Variant
aggrecan core protein isoform 3 precursor NP_001356197.1:p.Ser2508= S (Ser) > S (Ser) Synonymous Variant
ACAN transcript variant 2 NM_013227.4:c.7410C>T S [TCC] > S [TCT] Coding Sequence Variant
aggrecan core protein isoform 2 precursor NP_037359.3:p.Ser2470= S (Ser) > S (Ser) Synonymous Variant
ACAN transcript variant X1 XM_047432214.1:c.7410C>T S [TCC] > S [TCT] Coding Sequence Variant
aggrecan core protein isoform X1 XP_047288170.1:p.Ser2470= S (Ser) > S (Ser) Synonymous Variant
ACAN transcript variant X2 XM_047432215.1:c.7410C>T S [TCC] > S [TCT] Coding Sequence Variant
aggrecan core protein isoform X2 XP_047288171.1:p.Ser2470= S (Ser) > S (Ser) Synonymous Variant
ACAN transcript variant X3 XM_011521313.2:c.7410C>T S [TCC] > S [TCT] Coding Sequence Variant
aggrecan core protein isoform X3 XP_011519615.1:p.Ser2470= S (Ser) > S (Ser) Synonymous Variant
ACAN transcript variant X3 XM_047432216.1:c.7296C>T S [TCC] > S [TCT] Coding Sequence Variant
aggrecan core protein isoform X3 XP_047288172.1:p.Ser2432= S (Ser) > S (Ser) Synonymous Variant
ACAN transcript variant X4 XM_047432217.1:c.7296C>T S [TCC] > S [TCT] Coding Sequence Variant
aggrecan core protein isoform X3 XP_047288173.1:p.Ser2432= S (Ser) > S (Ser) Synonymous Variant
ACAN transcript variant X6 XM_011521314.2:c.7296C>T S [TCC] > S [TCT] Coding Sequence Variant
aggrecan core protein isoform X5 XP_011519616.1:p.Ser2432= S (Ser) > S (Ser) 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.

Allele: T (allele ID: 268091 )
ClinVar Accession Disease Names Clinical Significance
RCV000374956.3 not specified Benign
RCV000909439.9 not provided Benign
RCV002253348.1 Spondyloepiphyseal dysplasia, Kimberley type Benign
RCV002253349.1 Spondyloepimetaphyseal dysplasia, aggrecan type Benign
RCV002253350.1 Short stature and advanced bone age, with or without early-onset osteoarthritis and/or osteochondritis dissecans 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 C= T
GRCh38.p14 chr 15 NC_000015.10:g.88873918= NC_000015.10:g.88873918C>T
GRCh37.p13 chr 15 NC_000015.9:g.89417149= NC_000015.9:g.89417149C>T
ACAN RefSeqGene NG_012794.1:g.75476= NG_012794.1:g.75476C>T
ACAN transcript variant 2 NM_013227.4:c.7410= NM_013227.4:c.7410C>T
ACAN transcript variant 2 NM_013227.3:c.7410= NM_013227.3:c.7410C>T
ACAN transcript variant 3 NM_001369268.1:c.7524= NM_001369268.1:c.7524C>T
ACAN transcript variant X3 XM_011521313.2:c.7410= XM_011521313.2:c.7410C>T
ACAN transcript variant X6 XM_011521314.2:c.7296= XM_011521314.2:c.7296C>T
ACAN transcript variant 5 NM_001411097.1:c.7410= NM_001411097.1:c.7410C>T
ACAN transcript variant 4 NM_001411096.1:c.7296= NM_001411096.1:c.7296C>T
ACAN transcript variant X3 XM_047432216.1:c.7296= XM_047432216.1:c.7296C>T
ACAN transcript variant X1 XM_047432214.1:c.7410= XM_047432214.1:c.7410C>T
ACAN transcript variant X2 XM_047432215.1:c.7410= XM_047432215.1:c.7410C>T
ACAN transcript variant X4 XM_047432217.1:c.7296= XM_047432217.1:c.7296C>T
aggrecan core protein isoform 2 precursor NP_037359.3:p.Ser2470= NP_037359.3:p.Ser2470=
aggrecan core protein isoform 3 precursor NP_001356197.1:p.Ser2508= NP_001356197.1:p.Ser2508=
aggrecan core protein isoform X3 XP_011519615.1:p.Ser2470= XP_011519615.1:p.Ser2470=
aggrecan core protein isoform X5 XP_011519616.1:p.Ser2432= XP_011519616.1:p.Ser2432=
aggrecan core protein isoform X3 XP_047288172.1:p.Ser2432= XP_047288172.1:p.Ser2432=
aggrecan core protein isoform X1 XP_047288170.1:p.Ser2470= XP_047288170.1:p.Ser2470=
aggrecan core protein isoform X2 XP_047288171.1:p.Ser2470= XP_047288171.1:p.Ser2470=
aggrecan core protein isoform X3 XP_047288173.1:p.Ser2432= XP_047288173.1:p.Ser2432=
ACAN transcript variant 1 NM_001135.3:c.7220-487= NM_001135.3:c.7220-487C>T
ACAN transcript variant 1 NM_001135.4:c.7220-487= NM_001135.4:c.7220-487C>T
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#.

30 SubSNP, 13 Frequency, 5 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss464333640 Sep 17, 2011 (135)
2 CLINSEQ_SNP ss491706805 May 04, 2012 (137)
3 NHLBI-ESP ss713253469 Apr 25, 2013 (138)
4 EVA-GONL ss992060804 Aug 21, 2014 (142)
5 1000GENOMES ss1354529004 Aug 21, 2014 (142)
6 EVA_UK10K_ALSPAC ss1633567638 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1676561671 Apr 01, 2015 (144)
8 EVA_EXAC ss1691982870 Apr 01, 2015 (144)
9 EVA_MGP ss1711408781 Apr 01, 2015 (144)
10 CLINVAR ss2136849013 Dec 04, 2016 (149)
11 HUMAN_LONGEVITY ss2208934680 Dec 20, 2016 (150)
12 GNOMAD ss2741489319 Nov 08, 2017 (151)
13 GNOMAD ss2749378963 Nov 08, 2017 (151)
14 GNOMAD ss2937964806 Nov 08, 2017 (151)
15 SWEGEN ss3013718071 Nov 08, 2017 (151)
16 EGCUT_WGS ss3680849400 Jul 13, 2019 (153)
17 EVA_DECODE ss3698416180 Jul 13, 2019 (153)
18 KHV_HUMAN_GENOMES ss3818719716 Jul 13, 2019 (153)
19 EVA ss3824951104 Apr 27, 2020 (154)
20 EVA ss3825865704 Apr 27, 2020 (154)
21 EVA ss3834364470 Apr 27, 2020 (154)
22 TOPMED ss5000751461 Apr 26, 2021 (155)
23 1000G_HIGH_COVERAGE ss5299380776 Oct 16, 2022 (156)
24 EVA ss5420951432 Oct 16, 2022 (156)
25 HUGCELL_USP ss5492999588 Oct 16, 2022 (156)
26 1000G_HIGH_COVERAGE ss5601254824 Oct 16, 2022 (156)
27 EVA ss5828563246 Oct 16, 2022 (156)
28 EVA ss5848410113 Oct 16, 2022 (156)
29 EVA ss5876948490 Oct 16, 2022 (156)
30 EVA ss5949458635 Oct 16, 2022 (156)
31 1000Genomes NC_000015.9 - 89417149 Oct 12, 2018 (152)
32 1000Genomes_30x NC_000015.10 - 88873918 Oct 16, 2022 (156)
33 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 89417149 Oct 12, 2018 (152)
34 Genetic variation in the Estonian population NC_000015.9 - 89417149 Oct 12, 2018 (152)
35 ExAC NC_000015.9 - 89417149 Oct 12, 2018 (152)
36 gnomAD - Genomes NC_000015.10 - 88873918 Apr 26, 2021 (155)
37 gnomAD - Exomes NC_000015.9 - 89417149 Jul 13, 2019 (153)
38 GO Exome Sequencing Project NC_000015.9 - 89417149 Oct 12, 2018 (152)
39 Genome of the Netherlands Release 5 NC_000015.9 - 89417149 Apr 27, 2020 (154)
40 Medical Genome Project healthy controls from Spanish population NC_000015.9 - 89417149 Apr 27, 2020 (154)
41 TopMed NC_000015.10 - 88873918 Apr 26, 2021 (155)
42 UK 10K study - Twins NC_000015.9 - 89417149 Oct 12, 2018 (152)
43 ALFA NC_000015.10 - 88873918 Apr 26, 2021 (155)
44 ClinVar RCV000374956.3 Oct 16, 2022 (156)
45 ClinVar RCV000909439.9 Oct 16, 2022 (156)
46 ClinVar RCV002253348.1 Oct 16, 2022 (156)
47 ClinVar RCV002253349.1 Oct 16, 2022 (156)
48 ClinVar RCV002253350.1 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
ss491706805 NC_000015.8:87218152:C:T NC_000015.10:88873917:C:T (self)
67638490, 37562895, 26587648, 2367957, 10757360, 1408347, 16760994, 524541, 37562895, ss464333640, ss713253469, ss992060804, ss1354529004, ss1633567638, ss1676561671, ss1691982870, ss1711408781, ss2741489319, ss2749378963, ss2937964806, ss3013718071, ss3680849400, ss3824951104, ss3825865704, ss3834364470, ss5420951432, ss5828563246, ss5848410113, ss5949458635 NC_000015.9:89417148:C:T NC_000015.10:88873917:C:T (self)
RCV000374956.3, RCV000909439.9, RCV002253348.1, RCV002253349.1, RCV002253350.1, 88780759, 476878431, 216297121, 10408434295, ss2136849013, ss2208934680, ss3698416180, ss3818719716, ss5000751461, ss5299380776, ss5492999588, ss5601254824, ss5876948490 NC_000015.10:88873917:C:T NC_000015.10:88873917: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 rs190361551

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