Name: rs12798548
Published: September 21, 2022
License: Open Access

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.

rs12798548

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:1021099 (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=0.076168 (20161/264690, TOPMED)
T=0.079745 (11177/140160, GnomAD)
T=0.07660 (1447/18890, ALFA) (+ 14 more)
T=0.0551 (353/6404, 1000G_30x)
T=0.0529 (265/5008, 1000G)
T=0.0647 (290/4480, Estonian)
T=0.0843 (325/3854, ALSPAC)
T=0.0895 (332/3708, TWINSUK)
T=0.0000 (0/2922, KOREAN)
T=0.084 (84/998, GoNL)
T=0.063 (38/600, NorthernSweden)
T=0.007 (4/534, MGP)
T=0.106 (23/216, Qatari)
C=0.43 (19/44, SGDP_PRJ)
T=0.12 (5/40, GENOME_DK)
C=0.5 (3/6, Siberian)
T=0.5 (3/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MUC6 : 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	18890	C=0.92340	T=0.07660
European	Sub	14286	C=0.92265	T=0.07735
African	Sub	2946	C=0.9158	T=0.0842
African Others	Sub	114	C=0.886	T=0.114
African American	Sub	2832	C=0.9170	T=0.0830
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=0.849	T=0.151
Latin American 2	Sub	610	C=0.954	T=0.046
South Asian	Sub	98	C=0.96	T=0.04
Other	Sub	692	C=0.942	T=0.058

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.923832	T=0.076168
gnomAD - Genomes	Global	Study-wide	140160	C=0.920255	T=0.079745
gnomAD - Genomes	European	Sub	75884	C=0.91757	T=0.08243
gnomAD - Genomes	African	Sub	42010	C=0.91464	T=0.08536
gnomAD - Genomes	American	Sub	13660	C=0.93682	T=0.06318
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.9094	T=0.0906
gnomAD - Genomes	East Asian	Sub	3134	C=0.9987	T=0.0013
gnomAD - Genomes	Other	Sub	2150	C=0.9219	T=0.0781
Allele Frequency Aggregator	Total	Global	18890	C=0.92340	T=0.07660
Allele Frequency Aggregator	European	Sub	14286	C=0.92265	T=0.07735
Allele Frequency Aggregator	African	Sub	2946	C=0.9158	T=0.0842
Allele Frequency Aggregator	Other	Sub	692	C=0.942	T=0.058
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.954	T=0.046
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.849	T=0.151
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.96	T=0.04
1000Genomes_30x	Global	Study-wide	6404	C=0.9449	T=0.0551
1000Genomes_30x	African	Sub	1786	C=0.9110	T=0.0890
1000Genomes_30x	Europe	Sub	1266	C=0.9155	T=0.0845
1000Genomes_30x	South Asian	Sub	1202	C=0.9800	T=0.0200
1000Genomes_30x	East Asian	Sub	1170	C=0.9991	T=0.0009
1000Genomes_30x	American	Sub	980	C=0.937	T=0.063
1000Genomes	Global	Study-wide	5008	C=0.9471	T=0.0529
1000Genomes	African	Sub	1322	C=0.9130	T=0.0870
1000Genomes	East Asian	Sub	1008	C=0.9990	T=0.0010
1000Genomes	Europe	Sub	1006	C=0.9125	T=0.0875
1000Genomes	South Asian	Sub	978	C=0.981	T=0.019
1000Genomes	American	Sub	694	C=0.939	T=0.061
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9353	T=0.0647
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9157	T=0.0843
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9105	T=0.0895
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=1.0000	T=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.916	T=0.084
Northern Sweden	ACPOP	Study-wide	600	C=0.937	T=0.063
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.993	T=0.007
Qatari	Global	Study-wide	216	C=0.894	T=0.106
SGDP_PRJ	Global	Study-wide	44	C=0.43	T=0.57
The Danish reference pan genome	Danish	Study-wide	40	C=0.88	T=0.12
Siberian	Global	Study-wide	6	C=0.5	T=0.5

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.1021099C>T
GRCh37.p13 chr 11	NC_000011.9:g.1021099C>T
MUC6 RefSeqGene	NG_052845.1:g.20608G>A
GRCh38.p14 chr 11 fix patch HG107_HG2565_PATCH	NW_015148966.2:g.17840C>T
GRCh38.p14 chr 11 alt locus HSCHR11_3_CTG1	NT_187681.1:g.95492C>T
GRCh38.p14 chr 11 alt locus HSCHR11_2_CTG1	NT_187656.1:g.90664C>T

Gene: MUC6, mucin 6, oligomeric mucus/gel-forming (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MUC6 transcript	NM_005961.3:c.3589+116G>A	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

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 11	NC_000011.10:g.1021099=	NC_000011.10:g.1021099C>T
GRCh37.p13 chr 11	NC_000011.9:g.1021099=	NC_000011.9:g.1021099C>T
MUC6 RefSeqGene	NG_052845.1:g.20608=	NG_052845.1:g.20608G>A
GRCh38.p14 chr 11 fix patch HG107_HG2565_PATCH	NW_015148966.2:g.17840=	NW_015148966.2:g.17840C>T
GRCh38.p14 chr 11 alt locus HSCHR11_3_CTG1	NT_187681.1:g.95492=	NT_187681.1:g.95492C>T
GRCh38.p14 chr 11 alt locus HSCHR11_2_CTG1	NT_187656.1:g.90664=	NT_187656.1:g.90664C>T
MUC6 transcript	NM_005961.2:c.3589+116=	NM_005961.2:c.3589+116G>A
MUC6 transcript	NM_005961.3:c.3589+116=	NM_005961.3:c.3589+116G>A

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#.

55 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss20805984	Apr 05, 2004 (121)
2	ABI	ss43535960	Mar 14, 2006 (126)
3	1000GENOMES	ss109902529	Jan 24, 2009 (130)
4	ILLUMINA-UK	ss118441313	Feb 14, 2009 (130)
5	ENSEMBL	ss143180946	Dec 01, 2009 (131)
6	1000GENOMES	ss225045906	Jul 14, 2010 (132)
7	1000GENOMES	ss235411195	Jul 15, 2010 (132)
8	BL	ss254812663	May 09, 2011 (134)
9	TISHKOFF	ss562329880	Apr 25, 2013 (138)
10	EVA-GONL	ss988119056	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1077439745	Aug 21, 2014 (142)
12	1000GENOMES	ss1339794509	Aug 21, 2014 (142)
13	EVA_GENOME_DK	ss1575469106	Apr 01, 2015 (144)
14	EVA_DECODE	ss1597797840	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1625828006	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1668822039	Apr 01, 2015 (144)
17	EVA_MGP	ss1711277249	Apr 01, 2015 (144)
18	HAMMER_LAB	ss1806654699	Sep 08, 2015 (146)
19	WEILL_CORNELL_DGM	ss1931480180	Feb 12, 2016 (147)
20	JJLAB	ss2026480381	Sep 14, 2016 (149)
21	USC_VALOUEV	ss2154765850	Dec 20, 2016 (150)
22	HUMAN_LONGEVITY	ss2179577505	Dec 20, 2016 (150)
23	GNOMAD	ss2895426383	Nov 08, 2017 (151)
24	SWEGEN	ss3007456686	Nov 08, 2017 (151)
25	BIOINF_KMB_FNS_UNIBA	ss3027032530	Nov 08, 2017 (151)
26	CSHL	ss3349407974	Nov 08, 2017 (151)
27	URBANLAB	ss3649511293	Oct 12, 2018 (152)
28	EGCUT_WGS	ss3674864975	Jul 13, 2019 (153)
29	EVA_DECODE	ss3691055865	Jul 13, 2019 (153)
30	ACPOP	ss3737845132	Jul 13, 2019 (153)
31	EVA	ss3748841628	Jul 13, 2019 (153)
32	PACBIO	ss3786840015	Jul 13, 2019 (153)
33	PACBIO	ss3791996483	Jul 13, 2019 (153)
34	PACBIO	ss3796878655	Jul 13, 2019 (153)
35	KHV_HUMAN_GENOMES	ss3814191110	Jul 13, 2019 (153)
36	EVA	ss3832431640	Apr 26, 2020 (154)
37	EVA	ss3839758148	Apr 26, 2020 (154)
38	EVA	ss3845233889	Apr 26, 2020 (154)
39	SGDP_PRJ	ss3875461661	Apr 26, 2020 (154)
40	KRGDB	ss3923678644	Apr 26, 2020 (154)
41	FSA-LAB	ss3983992229	Apr 26, 2021 (155)
42	EVA	ss3986508510	Apr 26, 2021 (155)
43	TOPMED	ss4872575327	Apr 26, 2021 (155)
44	1000G_HIGH_COVERAGE	ss5286117394	Oct 16, 2022 (156)
45	EVA	ss5397234059	Oct 16, 2022 (156)
46	HUGCELL_USP	ss5481466447	Oct 16, 2022 (156)
47	EVA	ss5510225455	Oct 16, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5581105175	Oct 16, 2022 (156)
49	EVA	ss5624015729	Oct 16, 2022 (156)
50	SANFORD_IMAGENETICS	ss5650467247	Oct 16, 2022 (156)
51	YY_MCH	ss5812053727	Oct 16, 2022 (156)
52	EVA	ss5836145479	Oct 16, 2022 (156)
53	EVA	ss5848313849	Oct 16, 2022 (156)
54	EVA	ss5918518470	Oct 16, 2022 (156)
55	EVA	ss5941777699	Oct 16, 2022 (156)
56	1000Genomes	NC_000011.9 - 1021099	Oct 12, 2018 (152)
57	1000Genomes_30x	NC_000011.10 - 1021099	Oct 16, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 1021099	Oct 12, 2018 (152)
59	Genetic variation in the Estonian population	NC_000011.9 - 1021099	Oct 12, 2018 (152)
60	The Danish reference pan genome	NC_000011.9 - 1021099	Apr 26, 2020 (154)
61	gnomAD - Genomes	NC_000011.10 - 1021099	Apr 26, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000011.9 - 1021099	Apr 26, 2020 (154)
63	KOREAN population from KRGDB	NC_000011.9 - 1021099	Apr 26, 2020 (154)
64	Medical Genome Project healthy controls from Spanish population	NC_000011.9 - 1021099	Apr 26, 2020 (154)
65	Northern Sweden	NC_000011.9 - 1021099	Jul 13, 2019 (153)
66	Qatari	NC_000011.9 - 1021099	Apr 26, 2020 (154)
67	SGDP_PRJ	NC_000011.9 - 1021099	Apr 26, 2020 (154)
68	Siberian	NC_000011.9 - 1021099	Apr 26, 2020 (154)
69	TopMed	NC_000011.10 - 1021099	Apr 26, 2021 (155)
70	UK 10K study - Twins	NC_000011.9 - 1021099	Oct 12, 2018 (152)
71	ALFA	NC_000011.10 - 1021099	Apr 26, 2021 (155)

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
ss109902529, ss118441313, ss254812663, ss1597797840	NC_000011.8:1011098:C:T	NC_000011.10:1021098:C:T	(self)
52266393, 29038681, 20603223, 2405710, 12943128, 30856038, 393009, 11129997, 13522110, 27478641, 7282204, 29038681, ss225045906, ss235411195, ss562329880, ss988119056, ss1077439745, ss1339794509, ss1575469106, ss1625828006, ss1668822039, ss1711277249, ss1806654699, ss1931480180, ss2026480381, ss2154765850, ss2895426383, ss3007456686, ss3349407974, ss3674864975, ss3737845132, ss3748841628, ss3786840015, ss3791996483, ss3796878655, ss3832431640, ss3839758148, ss3875461661, ss3923678644, ss3983992229, ss3986508510, ss5397234059, ss5510225455, ss5624015729, ss5650467247, ss5836145479, ss5848313849, ss5941777699	NC_000011.9:1021098:C:T	NC_000011.10:1021098:C:T	(self)
68631110, 369131343, 88120983, 7106701051, ss2179577505, ss3027032530, ss3649511293, ss3691055865, ss3814191110, ss3845233889, ss4872575327, ss5286117394, ss5481466447, ss5581105175, ss5812053727, ss5918518470	NC_000011.10:1021098:C:T	NC_000011.10:1021098:C:T	(self)
ss43535960, ss143180946	NT_009237.18:961098:C:T	NC_000011.10:1021098:C:T	(self)
ss20805984	NT_035113.5:967248:C:T	NC_000011.10:1021098:C:T	(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 rs12798548

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs12798548