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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.

rs747586248

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:102609981 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000004 (1/264690, TOPMED)
G=0.000008 (2/251442, GnomAD_exome)
G=0.000007 (1/140254, GnomAD) (+ 6 more)
G=0.000016 (2/121314, ExAC)
G=0.00092 (26/28258, 14KJPN)
G=0.00125 (21/16758, 8.3KJPN)
G=0.00000 (0/14050, ALFA)
G=0.0003 (1/2922, KOREAN)
G=0.0016 (3/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MMP20 : Synonymous Variant
LOC101928477 : Intron 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 A=1.00000 G=0.00000
European Sub 9690 A=1.0000 G=0.0000
African Sub 2898 A=1.0000 G=0.0000
African Others Sub 114 A=1.000 G=0.000
African American Sub 2784 A=1.0000 G=0.0000
Asian Sub 112 A=1.000 G=0.000
East Asian Sub 86 A=1.00 G=0.00
Other Asian Sub 26 A=1.00 G=0.00
Latin American 1 Sub 146 A=1.000 G=0.000
Latin American 2 Sub 610 A=1.000 G=0.000
South Asian Sub 98 A=1.00 G=0.00
Other Sub 496 A=1.000 G=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 A=0.999996 G=0.000004
gnomAD - Exomes Global Study-wide 251442 A=0.999992 G=0.000008
gnomAD - Exomes European Sub 135378 A=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 49004 A=0.99996 G=0.00004
gnomAD - Exomes American Sub 34588 A=1.00000 G=0.00000
gnomAD - Exomes African Sub 16256 A=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6138 A=1.0000 G=0.0000
gnomAD - Genomes Global Study-wide 140254 A=0.999993 G=0.000007
gnomAD - Genomes European Sub 75940 A=0.99999 G=0.00001
gnomAD - Genomes African Sub 42054 A=1.00000 G=0.00000
gnomAD - Genomes American Sub 13656 A=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3130 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2152 A=1.0000 G=0.0000
ExAC Global Study-wide 121314 A=0.999984 G=0.000016
ExAC Europe Sub 73314 A=1.00000 G=0.00000
ExAC Asian Sub 25136 A=0.99992 G=0.00008
ExAC American Sub 11562 A=1.00000 G=0.00000
ExAC African Sub 10398 A=1.00000 G=0.00000
ExAC Other Sub 904 A=1.000 G=0.000
14KJPN JAPANESE Study-wide 28258 A=0.99908 G=0.00092
8.3KJPN JAPANESE Study-wide 16758 A=0.99875 G=0.00125
Allele Frequency Aggregator Total Global 14050 A=1.00000 G=0.00000
Allele Frequency Aggregator European Sub 9690 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2898 A=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 G=0.000
Allele Frequency Aggregator Other Sub 496 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9997 G=0.0003
Korean Genome Project KOREAN Study-wide 1832 A=0.9984 G=0.0016
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 11 NC_000011.10:g.102609981A>G
GRCh37.p13 chr 11 NC_000011.9:g.102480712A>G
MMP20 RefSeqGene NG_012151.1:g.20352T>C
Gene: MMP20, matrix metallopeptidase 20 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MMP20 transcript NM_004771.4:c.573T>C H [CAT] > H [CAC] Coding Sequence Variant
matrix metalloproteinase-20 preproprotein NP_004762.2:p.His191= H (His) > H (His) Synonymous Variant
Gene: LOC101928477, uncharacterized LOC101928477 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC101928477 transcript variant X4 XR_001748340.2:n. N/A Intron Variant
LOC101928477 transcript variant X5 XR_001748341.2:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X2 XR_007062866.1:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X6 XR_007062867.1:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X1 XR_947957.3:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X3 XR_947958.3:n. N/A Genic Upstream Transcript 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 A= G
GRCh38.p14 chr 11 NC_000011.10:g.102609981= NC_000011.10:g.102609981A>G
GRCh37.p13 chr 11 NC_000011.9:g.102480712= NC_000011.9:g.102480712A>G
MMP20 RefSeqGene NG_012151.1:g.20352= NG_012151.1:g.20352T>C
MMP20 transcript NM_004771.4:c.573= NM_004771.4:c.573T>C
MMP20 transcript NM_004771.3:c.573= NM_004771.3:c.573T>C
matrix metalloproteinase-20 preproprotein NP_004762.2:p.His191= NP_004762.2:p.His191=
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#.

9 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1690605727 Apr 01, 2015 (144)
2 GNOMAD ss2739346038 Nov 08, 2017 (151)
3 KRGDB ss3925455718 Apr 26, 2020 (154)
4 KOGIC ss3970631243 Apr 26, 2020 (154)
5 EVA ss3986542989 Apr 26, 2021 (155)
6 GNOMAD ss4241435589 Apr 26, 2021 (155)
7 TOPMED ss4897823395 Apr 26, 2021 (155)
8 TOMMO_GENOMICS ss5203620002 Apr 26, 2021 (155)
9 TOMMO_GENOMICS ss5751990352 Oct 16, 2022 (156)
10 ExAC NC_000011.9 - 102480712 Oct 12, 2018 (152)
11 gnomAD - Genomes NC_000011.10 - 102609981 Apr 26, 2021 (155)
12 gnomAD - Exomes NC_000011.9 - 102480712 Jul 13, 2019 (153)
13 KOREAN population from KRGDB NC_000011.9 - 102480712 Apr 26, 2020 (154)
14 Korean Genome Project NC_000011.10 - 102609981 Apr 26, 2020 (154)
15 8.3KJPN NC_000011.9 - 102480712 Apr 26, 2021 (155)
16 14KJPN NC_000011.10 - 102609981 Oct 16, 2022 (156)
17 TopMed NC_000011.10 - 102609981 Apr 26, 2021 (155)
18 ALFA NC_000011.10 - 102609981 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
879342, 8563375, 32633112, 61589309, ss1690605727, ss2739346038, ss3925455718, ss3986542989, ss5203620002 NC_000011.9:102480711:A:G NC_000011.10:102609980:A:G (self)
390197981, 27009244, 85827456, 113369051, 7830397690, ss3970631243, ss4241435589, ss4897823395, ss5751990352 NC_000011.10:102609980:A:G NC_000011.10:102609980:A:G (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 rs747586248

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