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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 Aliases 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.

rs5015147

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr12:40418590 (GRCh38.p12) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.03179 (3992/125568, TOPMED)
A=0.0248 (778/31340, GnomAD)
A=0.060 (298/5008, 1000G) (+ 5 more)
A=0.025 (111/4480, Estonian)
A=0.018 (68/3854, ALSPAC)
A=0.018 (68/3708, TWINSUK)
A=0.02 (10/600, NorthernSweden)
A=0.06 (14/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MUC19 : Intron Variant
LOC105369736 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 12 NC_000012.12:g.40418590G>A
GRCh37.p13 chr 12 NC_000012.11:g.40812392G>A
Gene: MUC19, mucin 19, oligomeric (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MUC19 transcript NM_173600.2:c. N/A Intron Variant
Gene: LOC105369736, uncharacterized LOC105369736 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105369736 transcript variant X5 XR_001749087.1:n. N/A Intron Variant
LOC105369736 transcript variant X6 XR_001749088.1:n. N/A Intron Variant
LOC105369736 transcript variant X2 XR_944866.1:n. N/A Intron Variant
LOC105369736 transcript variant X3 XR_944867.1:n. N/A Intron Variant
LOC105369736 transcript variant X4 XR_944868.2:n. N/A Intron Variant
LOC105369736 transcript variant X1 XR_944869.2:n. N/A Intron 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

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 125568 G=0.96821 A=0.03179
gnomAD - Genomes Global Study-wide 31340 G=0.9752 A=0.0248
gnomAD - Genomes European Sub 18858 G=0.9774 A=0.0226
gnomAD - Genomes African Sub 8708 G=0.993 A=0.007
gnomAD - Genomes East Asian Sub 1560 G=0.964 A=0.036
gnomAD - Genomes Other Sub 1082 G=0.967 A=0.033
gnomAD - Genomes American Sub 842 G=0.79 A=0.21
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.94 A=0.06
1000Genomes Global Study-wide 5008 G=0.940 A=0.060
1000Genomes African Sub 1322 G=0.997 A=0.003
1000Genomes East Asian Sub 1008 G=0.939 A=0.061
1000Genomes Europe Sub 1006 G=0.977 A=0.023
1000Genomes South Asian Sub 978 G=0.90 A=0.10
1000Genomes American Sub 694 G=0.84 A=0.16
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.975 A=0.025
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.982 A=0.018
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.982 A=0.018
Northern Sweden ACPOP Study-wide 600 G=0.98 A=0.02
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.94 A=0.06
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 G= A Note
GRCh38.p12 chr 12 NC_000012.12:g.40418590= NC_000012.12:g.40418590G>A
GRCh37.p13 chr 12 NC_000012.11:g.40812392= NC_000012.11:g.40812392G>A
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#.

29 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss235906175 Jul 15, 2010 (132)
2 SSMP ss658666228 Apr 25, 2013 (138)
3 EVA-GONL ss989452955 Aug 21, 2014 (142)
4 JMKIDD_LAB ss1078403299 Aug 21, 2014 (142)
5 1000GENOMES ss1344704143 Aug 21, 2014 (142)
6 DDI ss1426910597 Apr 01, 2015 (144)
7 EVA_GENOME_DK ss1576236121 Apr 01, 2015 (144)
8 EVA_DECODE ss1599120305 Apr 01, 2015 (144)
9 EVA_UK10K_ALSPAC ss1628430237 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1671424270 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1932816692 Feb 12, 2016 (147)
12 GENOMED ss1967572078 Jul 19, 2016 (147)
13 JJLAB ss2027158990 Sep 14, 2016 (149)
14 ILLUMINA ss2094873666 Dec 20, 2016 (150)
15 ILLUMINA ss2095034396 Dec 20, 2016 (150)
16 USC_VALOUEV ss2155492103 Dec 20, 2016 (150)
17 HUMAN_LONGEVITY ss2189144339 Dec 20, 2016 (150)
18 TOPMED ss2353067225 Dec 20, 2016 (150)
19 GRF ss2699831359 Nov 08, 2017 (151)
20 GNOMAD ss2909608316 Nov 08, 2017 (151)
21 SWEGEN ss3009556370 Nov 08, 2017 (151)
22 TOPMED ss3168843942 Nov 08, 2017 (151)
23 ILLUMINA ss3651799533 Oct 12, 2018 (152)
24 EGCUT_WGS ss3676832014 Jul 13, 2019 (153)
25 EVA_DECODE ss3693517975 Jul 13, 2019 (153)
26 ACPOP ss3738952204 Jul 13, 2019 (153)
27 ILLUMINA ss3744394211 Jul 13, 2019 (153)
28 EVA ss3750384198 Jul 13, 2019 (153)
29 KHV_HUMAN_GENOMES ss3815713172 Jul 13, 2019 (153)
30 1000Genomes NC_000012.11 - 40812392 Oct 12, 2018 (152)
31 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 40812392 Oct 12, 2018 (152)
32 Genetic variation in the Estonian population NC_000012.11 - 40812392 Oct 12, 2018 (152)
33 gnomAD - Genomes NC_000012.11 - 40812392 Jul 13, 2019 (153)
34 Northern Sweden NC_000012.11 - 40812392 Jul 13, 2019 (153)
35 TopMed NC_000012.12 - 40418590 Oct 12, 2018 (152)
36 UK 10K study - Twins NC_000012.11 - 40812392 Oct 12, 2018 (152)
37 A Vietnamese Genetic Variation Database NC_000012.11 - 40812392 Jul 13, 2019 (153)
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
ss1599120305, ss2094873666 NC_000012.10:39098658:G:A NC_000012.12:40418589:G:A (self)
57441332, 31897662, 22570262, 156768953, 12237069, 31897662, 7078998, ss235906175, ss658666228, ss989452955, ss1078403299, ss1344704143, ss1426910597, ss1576236121, ss1628430237, ss1671424270, ss1932816692, ss1967572078, ss2027158990, ss2095034396, ss2155492103, ss2353067225, ss2699831359, ss2909608316, ss3009556370, ss3651799533, ss3676832014, ss3738952204, ss3744394211, ss3750384198 NC_000012.11:40812391:G:A NC_000012.12:40418589:G:A (self)
82097916, ss2189144339, ss3168843942, ss3693517975, ss3815713172 NC_000012.12:40418589:G:A NC_000012.12:40418589:G:A (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 rs5015147

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.post308+0fe9b3b