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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.

rs538486886

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:88874434 (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=0.000004 (1/264690, TOPMED)
T=0.000021 (5/235544, GnomAD_exome)
T=0.000007 (1/140212, GnomAD) (+ 4 more)
T=0.00005 (3/64364, ExAC)
T=0.00000 (0/14050, ALFA)
T=0.0002 (1/6404, 1000G_30x)
T=0.0002 (1/5008, 1000G)
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 14050 C=1.00000 T=0.00000
European Sub 9690 C=1.0000 T=0.0000
African Sub 2898 C=1.0000 T=0.0000
African Others Sub 114 C=1.000 T=0.000
African American Sub 2784 C=1.0000 T=0.0000
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 496 C=1.000 T=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 T=0.000004
gnomAD - Exomes Global Study-wide 235544 C=0.999979 T=0.000021
gnomAD - Exomes European Sub 126742 C=0.999992 T=0.000008
gnomAD - Exomes Asian Sub 45764 C=0.99991 T=0.00009
gnomAD - Exomes American Sub 33300 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 14216 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9726 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 5796 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140212 C=0.999993 T=0.000007
gnomAD - Genomes European Sub 75926 C=0.99999 T=0.00001
gnomAD - Genomes African Sub 42030 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13650 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
ExAC Global Study-wide 64364 C=0.99995 T=0.00005
ExAC Europe Sub 39384 C=1.00000 T=0.00000
ExAC Asian Sub 14336 C=0.99979 T=0.00021
ExAC African Sub 5310 C=1.0000 T=0.0000
ExAC American Sub 4840 C=1.0000 T=0.0000
ExAC Other Sub 494 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 14050 C=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 9690 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2898 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Other Sub 496 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9998 T=0.0002
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=0.9992 T=0.0008
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9998 T=0.0002
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=0.999 T=0.001
1000Genomes American Sub 694 C=1.000 T=0.000
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.88874434C>T
GRCh37.p13 chr 15 NC_000015.9:g.89417665C>T
ACAN RefSeqGene NG_012794.1:g.75992C>T
Gene: ACAN, aggrecan (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ACAN transcript variant 3 NM_001369268.1:c.7660C>T R [CGG] > W [TGG] Coding Sequence Variant
aggrecan core protein isoform 3 precursor NP_001356197.1:p.Arg2554T…

NP_001356197.1:p.Arg2554Trp

R (Arg) > W (Trp) Missense Variant
ACAN transcript variant 2 NM_013227.4:c.7546C>T R [CGG] > W [TGG] Coding Sequence Variant
aggrecan core protein isoform 2 precursor NP_037359.3:p.Arg2516Trp R (Arg) > W (Trp) Missense Variant
ACAN transcript variant 1 NM_001135.4:c.7249C>T R [CGG] > W [TGG] Coding Sequence Variant
aggrecan core protein isoform 1 precursor NP_001126.3:p.Arg2417Trp R (Arg) > W (Trp) Missense Variant
ACAN transcript variant X1 XM_047432214.1:c. N/A Genic Downstream Transcript Variant
ACAN transcript variant X2 XM_047432215.1:c. N/A Genic Downstream Transcript Variant
ACAN transcript variant X3 XM_047432216.1:c. N/A Genic Downstream Transcript Variant
ACAN transcript variant X4 XM_047432217.1:c. N/A Genic Downstream Transcript Variant
ACAN transcript variant X3 XM_011521313.2:c.7546C>T R [CGG] > W [TGG] Coding Sequence Variant
aggrecan core protein isoform X3 XP_011519615.1:p.Arg2516T…

XP_011519615.1:p.Arg2516Trp

R (Arg) > W (Trp) Missense Variant
ACAN transcript variant X6 XM_011521314.2:c.7432C>T R [CGG] > W [TGG] Coding Sequence Variant
aggrecan core protein isoform X5 XP_011519616.1:p.Arg2478T…

XP_011519616.1:p.Arg2478Trp

R (Arg) > W (Trp) 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
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.88874434= NC_000015.10:g.88874434C>T
GRCh37.p13 chr 15 NC_000015.9:g.89417665= NC_000015.9:g.89417665C>T
ACAN RefSeqGene NG_012794.1:g.75992= NG_012794.1:g.75992C>T
ACAN transcript variant 2 NM_013227.4:c.7546= NM_013227.4:c.7546C>T
ACAN transcript variant 2 NM_013227.3:c.7546= NM_013227.3:c.7546C>T
ACAN transcript variant 1 NM_001135.4:c.7249= NM_001135.4:c.7249C>T
ACAN transcript variant 1 NM_001135.3:c.7249= NM_001135.3:c.7249C>T
ACAN transcript variant 3 NM_001369268.1:c.7660= NM_001369268.1:c.7660C>T
ACAN transcript variant X3 XM_011521313.2:c.7546= XM_011521313.2:c.7546C>T
ACAN transcript variant X6 XM_011521314.2:c.7432= XM_011521314.2:c.7432C>T
ACAN transcript variant 5 NM_001411097.1:c.7546= NM_001411097.1:c.7546C>T
ACAN transcript variant 4 NM_001411096.1:c.7432= NM_001411096.1:c.7432C>T
aggrecan core protein isoform 2 precursor NP_037359.3:p.Arg2516= NP_037359.3:p.Arg2516Trp
aggrecan core protein isoform 1 precursor NP_001126.3:p.Arg2417= NP_001126.3:p.Arg2417Trp
aggrecan core protein isoform 3 precursor NP_001356197.1:p.Arg2554= NP_001356197.1:p.Arg2554Trp
aggrecan core protein isoform X3 XP_011519615.1:p.Arg2516= XP_011519615.1:p.Arg2516Trp
aggrecan core protein isoform X5 XP_011519616.1:p.Arg2478= XP_011519616.1:p.Arg2478Trp
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#.

8 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1354529032 Aug 21, 2014 (142)
2 EVA_EXAC ss1691982935 Apr 01, 2015 (144)
3 GNOMAD ss2741489414 Nov 08, 2017 (151)
4 GNOMAD ss4293442996 Apr 26, 2021 (155)
5 TOPMED ss5000751600 Apr 26, 2021 (155)
6 EVA ss5420951475 Oct 16, 2022 (156)
7 1000G_HIGH_COVERAGE ss5601254855 Oct 16, 2022 (156)
8 EVA ss5876948518 Oct 16, 2022 (156)
9 1000Genomes NC_000015.9 - 89417665 Oct 12, 2018 (152)
10 1000Genomes_30x NC_000015.10 - 88874434 Oct 16, 2022 (156)
11 ExAC NC_000015.9 - 89417665 Oct 12, 2018 (152)
12 gnomAD - Genomes NC_000015.10 - 88874434 Apr 26, 2021 (155)
13 gnomAD - Exomes NC_000015.9 - 89417665 Jul 13, 2019 (153)
14 TopMed NC_000015.10 - 88874434 Apr 26, 2021 (155)
15 ALFA NC_000015.10 - 88874434 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
67638519, 2368025, 10757449, ss1354529032, ss1691982935, ss2741489414, ss5420951475 NC_000015.9:89417664:C:T NC_000015.10:88874433:C:T (self)
88780790, 476878543, 216297260, 373753029, ss4293442996, ss5000751600, ss5601254855, ss5876948518 NC_000015.10:88874433:C:T NC_000015.10:88874433: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 rs538486886

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