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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.


Current Build 153

Released July 9, 2019

Homo sapiens
chr12:40404550 (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.

Variation Type
SNV Single Nucleotide Variation
C=0.13183 (16554/125568, TOPMED)
C=0.1273 (3994/31372, GnomAD)
C=0.108 (540/5008, 1000G) (+ 4 more)
C=0.115 (514/4480, Estonian)
C=0.158 (610/3854, ALSPAC)
C=0.146 (540/3708, TWINSUK)
C=0.10 (63/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MUC19 : Intron Variant
LOC105369736 : Intron Variant
0 citations
Genomic View
See rs on genome

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.40404550T>C
GRCh37.p13 chr 12 NC_000012.11:g.40798352T>C
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

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

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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 T=0.86817 C=0.13183
gnomAD - Genomes Global Study-wide 31372 T=0.8727 C=0.1273
gnomAD - Genomes European Sub 18894 T=0.8688 C=0.1312
gnomAD - Genomes African Sub 8698 T=0.856 C=0.144
gnomAD - Genomes East Asian Sub 1558 T=1.000 C=0.000
gnomAD - Genomes Other Sub 1084 T=0.861 C=0.139
gnomAD - Genomes American Sub 848 T=0.91 C=0.09
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.86 C=0.14
1000Genomes Global Study-wide 5008 T=0.892 C=0.108
1000Genomes African Sub 1322 T=0.875 C=0.125
1000Genomes East Asian Sub 1008 T=0.999 C=0.001
1000Genomes Europe Sub 1006 T=0.854 C=0.146
1000Genomes South Asian Sub 978 T=0.82 C=0.18
1000Genomes American Sub 694 T=0.92 C=0.08
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.885 C=0.115
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.842 C=0.158
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.854 C=0.146
Northern Sweden ACPOP Study-wide 600 T=0.90 C=0.10

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 T= C Note
GRCh38.p12 chr 12 NC_000012.12:g.40404550= NC_000012.12:g.40404550T>C
GRCh37.p13 chr 12 NC_000012.11:g.40798352= NC_000012.11:g.40798352T>C

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#.

36 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss80960416 Dec 14, 2007 (129)
2 HGSV ss86090877 Dec 14, 2007 (129)
3 1000GENOMES ss113435405 Jan 25, 2009 (130)
4 ILLUMINA-UK ss118738000 Feb 14, 2009 (130)
5 COMPLETE_GENOMICS ss168174197 Jul 04, 2010 (132)
6 COMPLETE_GENOMICS ss169630213 Jul 04, 2010 (132)
7 1000GENOMES ss225713111 Jul 14, 2010 (132)
8 1000GENOMES ss235906112 Jul 15, 2010 (132)
9 TISHKOFF ss563120507 Apr 25, 2013 (138)
10 SSMP ss658666119 Apr 25, 2013 (138)
11 EVA-GONL ss989452800 Aug 21, 2014 (142)
12 JMKIDD_LAB ss1078403177 Aug 21, 2014 (142)
13 1000GENOMES ss1344703683 Aug 21, 2014 (142)
14 EVA_GENOME_DK ss1576236015 Apr 01, 2015 (144)
15 EVA_DECODE ss1599120125 Apr 01, 2015 (144)
16 EVA_UK10K_ALSPAC ss1628429958 Apr 01, 2015 (144)
17 EVA_UK10K_TWINSUK ss1671423991 Apr 01, 2015 (144)
18 HAMMER_LAB ss1807210675 Sep 08, 2015 (146)
19 WEILL_CORNELL_DGM ss1932816558 Feb 12, 2016 (147)
20 JJLAB ss2027158888 Sep 14, 2016 (149)
21 ILLUMINA ss2094873583 Dec 20, 2016 (150)
22 ILLUMINA ss2095034328 Dec 20, 2016 (150)
23 USC_VALOUEV ss2155491999 Dec 20, 2016 (150)
24 HUMAN_LONGEVITY ss2189143394 Dec 20, 2016 (150)
25 TOPMED ss2353066290 Dec 20, 2016 (150)
26 GNOMAD ss2909607155 Nov 08, 2017 (151)
27 SWEGEN ss3009556156 Nov 08, 2017 (151)
28 BIOINF_KMB_FNS_UNIBA ss3027387622 Nov 08, 2017 (151)
29 TOPMED ss3168841362 Nov 08, 2017 (151)
30 CSHL ss3350027969 Nov 08, 2017 (151)
31 ILLUMINA ss3651799450 Oct 12, 2018 (152)
32 EGCUT_WGS ss3676831785 Jul 13, 2019 (153)
33 EVA_DECODE ss3693517722 Jul 13, 2019 (153)
34 ACPOP ss3738952064 Jul 13, 2019 (153)
35 EVA ss3750384021 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3815713018 Jul 13, 2019 (153)
37 1000Genomes NC_000012.11 - 40798352 Oct 12, 2018 (152)
38 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 40798352 Oct 12, 2018 (152)
39 Genetic variation in the Estonian population NC_000012.11 - 40798352 Oct 12, 2018 (152)
40 gnomAD - Genomes NC_000012.11 - 40798352 Jul 13, 2019 (153)
41 Northern Sweden NC_000012.11 - 40798352 Jul 13, 2019 (153)
42 TopMed NC_000012.12 - 40404550 Oct 12, 2018 (152)
43 UK 10K study - Twins NC_000012.11 - 40798352 Oct 12, 2018 (152)

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
ss80960416, ss86090877 NC_000012.9:39084618:T:C NC_000012.12:40404549:T:C (self)
ss113435405, ss118738000, ss168174197, ss169630213, ss1599120125, ss2094873583 NC_000012.10:39084618:T:C NC_000012.12:40404549:T:C (self)
57440856, 31897360, 22570033, 156767781, 12236929, 31897360, ss225713111, ss235906112, ss563120507, ss658666119, ss989452800, ss1078403177, ss1344703683, ss1576236015, ss1628429958, ss1671423991, ss1807210675, ss1932816558, ss2027158888, ss2095034328, ss2155491999, ss2353066290, ss2909607155, ss3009556156, ss3350027969, ss3651799450, ss3676831785, ss3738952064, ss3750384021 NC_000012.11:40798351:T:C NC_000012.12:40404549:T:C (self)
82095622, ss2189143394, ss3027387622, ss3168841362, ss3693517722, ss3815713018 NC_000012.12:40404549:T:C NC_000012.12:40404549:T:C (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 rs57997594

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