Name: rs1492315
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.

rs1492315

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:40550300 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.236968 (62723/264690, TOPMED)
T=0.243517 (34104/140048, GnomAD)
T=0.19110 (5400/28258, 14KJPN) (+ 16 more)
T=0.22647 (4278/18890, ALFA)
T=0.18944 (3175/16760, 8.3KJPN)
T=0.2250 (1441/6404, 1000G_30x)
T=0.2177 (1090/5008, 1000G)
T=0.2513 (1126/4480, Estonian)
T=0.1725 (665/3854, ALSPAC)
T=0.1726 (640/3708, TWINSUK)
T=0.1540 (451/2928, KOREAN)
T=0.156 (156/998, GoNL)
T=0.177 (106/600, NorthernSweden)
T=0.013 (7/534, MGP)
T=0.227 (49/216, Qatari)
T=0.181 (39/216, Vietnamese)
A=0.380 (70/184, SGDP_PRJ)
T=0.12 (5/40, GENOME_DK)
A=0.45 (9/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MUC19 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18890	A=0.77353	T=0.22647
European	Sub	14286	A=0.79980	T=0.20020
African	Sub	2946	A=0.6212	T=0.3788
African Others	Sub	114	A=0.535	T=0.465
African American	Sub	2832	A=0.6246	T=0.3754
Asian	Sub	112	A=0.750	T=0.250
East Asian	Sub	86	A=0.76	T=0.24
Other Asian	Sub	26	A=0.73	T=0.27
Latin American 1	Sub	146	A=0.753	T=0.247
Latin American 2	Sub	610	A=0.836	T=0.164
South Asian	Sub	98	A=0.90	T=0.10
Other	Sub	692	A=0.815	T=0.185

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	A=0.763032	T=0.236968
gnomAD - Genomes	Global	Study-wide	140048	A=0.756483	T=0.243517
gnomAD - Genomes	European	Sub	75870	A=0.80887	T=0.19113
gnomAD - Genomes	African	Sub	41960	A=0.63644	T=0.36356
gnomAD - Genomes	American	Sub	13634	A=0.80915	T=0.19085
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.7702	T=0.2298
gnomAD - Genomes	East Asian	Sub	3108	A=0.8353	T=0.1647
gnomAD - Genomes	Other	Sub	2152	A=0.7816	T=0.2184
14KJPN	JAPANESE	Study-wide	28258	A=0.80890	T=0.19110
Allele Frequency Aggregator	Total	Global	18890	A=0.77353	T=0.22647
Allele Frequency Aggregator	European	Sub	14286	A=0.79980	T=0.20020
Allele Frequency Aggregator	African	Sub	2946	A=0.6212	T=0.3788
Allele Frequency Aggregator	Other	Sub	692	A=0.815	T=0.185
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.836	T=0.164
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.753	T=0.247
Allele Frequency Aggregator	Asian	Sub	112	A=0.750	T=0.250
Allele Frequency Aggregator	South Asian	Sub	98	A=0.90	T=0.10
8.3KJPN	JAPANESE	Study-wide	16760	A=0.81056	T=0.18944
1000Genomes_30x	Global	Study-wide	6404	A=0.7750	T=0.2250
1000Genomes_30x	African	Sub	1786	A=0.5991	T=0.4009
1000Genomes_30x	Europe	Sub	1266	A=0.8120	T=0.1880
1000Genomes_30x	South Asian	Sub	1202	A=0.9010	T=0.0990
1000Genomes_30x	East Asian	Sub	1170	A=0.8282	T=0.1718
1000Genomes_30x	American	Sub	980	A=0.830	T=0.170
1000Genomes	Global	Study-wide	5008	A=0.7823	T=0.2177
1000Genomes	African	Sub	1322	A=0.6135	T=0.3865
1000Genomes	East Asian	Sub	1008	A=0.8294	T=0.1706
1000Genomes	Europe	Sub	1006	A=0.8101	T=0.1899
1000Genomes	South Asian	Sub	978	A=0.901	T=0.099
1000Genomes	American	Sub	694	A=0.829	T=0.171
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7487	T=0.2513
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.8275	T=0.1725
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.8274	T=0.1726
KOREAN population from KRGDB	KOREAN	Study-wide	2928	A=0.8460	T=0.1540
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.844	T=0.156
Northern Sweden	ACPOP	Study-wide	600	A=0.823	T=0.177
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	A=0.987	T=0.013
Qatari	Global	Study-wide	216	A=0.773	T=0.227
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.819	T=0.181
SGDP_PRJ	Global	Study-wide	184	A=0.380	T=0.620
The Danish reference pan genome	Danish	Study-wide	40	A=0.88	T=0.12
Siberian	Global	Study-wide	20	A=0.45	T=0.55

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 12	NC_000012.12:g.40550300A>T
GRCh37.p13 chr 12	NC_000012.11:g.40944102A>T

Gene: MUC19, mucin 19, oligomeric (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MUC19 transcript	NM_173600.2:c.23339+142A>T	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	A=	T
GRCh38.p14 chr 12	NC_000012.12:g.40550300=	NC_000012.12:g.40550300A>T
GRCh37.p13 chr 12	NC_000012.11:g.40944102=	NC_000012.11:g.40944102A>T
MUC19 transcript	NM_173600.2:c.23339+142=	NM_173600.2:c.23339+142A>T
MUC19 transcript	XM_003846356.2:c.23342+142=	XM_003846356.2:c.23342+142A>T

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#.

58 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2319127	Oct 23, 2000 (88)
2	SC_SNP	ss16151599	Feb 27, 2004 (120)
3	ABI	ss38892126	Mar 15, 2006 (126)
4	1000GENOMES	ss111822198	Jan 25, 2009 (130)
5	1000GENOMES	ss113437492	Jan 25, 2009 (130)
6	COMPLETE_GENOMICS	ss169634221	Jul 04, 2010 (132)
7	BUSHMAN	ss198059627	Jul 04, 2010 (132)
8	BCM-HGSC-SUB	ss208245723	Jul 04, 2010 (132)
9	1000GENOMES	ss225713916	Jul 14, 2010 (132)
10	1000GENOMES	ss235906929	Jul 15, 2010 (132)
11	1000GENOMES	ss242469639	Jul 15, 2010 (132)
12	GMI	ss281365152	May 04, 2012 (137)
13	TISHKOFF	ss563121277	Apr 25, 2013 (138)
14	SSMP	ss658667219	Apr 25, 2013 (138)
15	EVA-GONL	ss989454301	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1078404162	Aug 21, 2014 (142)
17	1000GENOMES	ss1344708305	Aug 21, 2014 (142)
18	DDI	ss1426911220	Apr 01, 2015 (144)
19	EVA_GENOME_DK	ss1576237080	Apr 01, 2015 (144)
20	EVA_DECODE	ss1599121544	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1628432457	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1671426490	Apr 01, 2015 (144)
23	EVA_MGP	ss1711326928	Apr 01, 2015 (144)
24	HAMMER_LAB	ss1807211324	Sep 08, 2015 (146)
25	WEILL_CORNELL_DGM	ss1932817987	Feb 12, 2016 (147)
26	GENOMED	ss1967572523	Jul 19, 2016 (147)
27	JJLAB	ss2027159770	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2155493166	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2189152793	Dec 20, 2016 (150)
30	SYSTEMSBIOZJU	ss2628059223	Nov 08, 2017 (151)
31	GRF	ss2699832674	Nov 08, 2017 (151)
32	GNOMAD	ss2909620765	Nov 08, 2017 (151)
33	SWEGEN	ss3009559100	Nov 08, 2017 (151)
34	BIOINF_KMB_FNS_UNIBA	ss3027388147	Nov 08, 2017 (151)
35	CSHL	ss3350028851	Nov 08, 2017 (151)
36	EGCUT_WGS	ss3676833887	Jul 13, 2019 (153)
37	EVA_DECODE	ss3693520271	Jul 13, 2019 (153)
38	ACPOP	ss3738953436	Jul 13, 2019 (153)
39	EVA	ss3750385648	Jul 13, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3815714599	Jul 13, 2019 (153)
41	EVA	ss3833083581	Apr 27, 2020 (154)
42	SGDP_PRJ	ss3878114815	Apr 27, 2020 (154)
43	KRGDB	ss3926721066	Apr 27, 2020 (154)
44	TOPMED	ss4915585923	Apr 26, 2021 (155)
45	TOMMO_GENOMICS	ss5205965802	Apr 26, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5290536814	Oct 13, 2022 (156)
47	EVA	ss5405152337	Oct 13, 2022 (156)
48	HUGCELL_USP	ss5485324113	Oct 13, 2022 (156)
49	EVA	ss5510672787	Oct 13, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5587890687	Oct 13, 2022 (156)
51	SANFORD_IMAGENETICS	ss5652999997	Oct 13, 2022 (156)
52	TOMMO_GENOMICS	ss5755652195	Oct 13, 2022 (156)
53	YY_MCH	ss5813229585	Oct 13, 2022 (156)
54	EVA	ss5837864432	Oct 13, 2022 (156)
55	EVA	ss5850347553	Oct 13, 2022 (156)
56	EVA	ss5904084394	Oct 13, 2022 (156)
57	EVA	ss5944357764	Oct 13, 2022 (156)
58	EVA	ss5981275014	Oct 13, 2022 (156)
59	1000Genomes	NC_000012.11 - 40944102	Oct 12, 2018 (152)
60	1000Genomes_30x	NC_000012.12 - 40550300	Oct 13, 2022 (156)
61	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 40944102	Oct 12, 2018 (152)
62	Genetic variation in the Estonian population	NC_000012.11 - 40944102	Oct 12, 2018 (152)
63	The Danish reference pan genome	NC_000012.11 - 40944102	Apr 27, 2020 (154)
64	gnomAD - Genomes	NC_000012.12 - 40550300	Apr 26, 2021 (155)
65	Genome of the Netherlands Release 5	NC_000012.11 - 40944102	Apr 27, 2020 (154)
66	KOREAN population from KRGDB	NC_000012.11 - 40944102	Apr 27, 2020 (154)
67	Medical Genome Project healthy controls from Spanish population	NC_000012.11 - 40944102	Apr 27, 2020 (154)
68	Northern Sweden	NC_000012.11 - 40944102	Jul 13, 2019 (153)
69	Qatari	NC_000012.11 - 40944102	Apr 27, 2020 (154)
70	SGDP_PRJ	NC_000012.11 - 40944102	Apr 27, 2020 (154)
71	Siberian	NC_000012.11 - 40944102	Apr 27, 2020 (154)
72	8.3KJPN	NC_000012.11 - 40944102	Apr 26, 2021 (155)
73	14KJPN	NC_000012.12 - 40550300	Oct 13, 2022 (156)
74	TopMed	NC_000012.12 - 40550300	Apr 26, 2021 (155)
75	UK 10K study - Twins	NC_000012.11 - 40944102	Oct 12, 2018 (152)
76	A Vietnamese Genetic Variation Database	NC_000012.11 - 40944102	Jul 13, 2019 (153)
77	ALFA	NC_000012.12 - 40550300	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
ss111822198, ss113437492, ss169634221, ss198059627, ss208245723, ss281365152, ss1599121544	NC_000012.10:39230368:A:T	NC_000012.12:40550299:A:T	(self)
57445637, 31900084, 22572135, 2933047, 14236975, 33898460, 442688, 12238301, 14859917, 30131795, 8009520, 63935109, 31900084, 7079730, ss225713916, ss235906929, ss242469639, ss563121277, ss658667219, ss989454301, ss1078404162, ss1344708305, ss1426911220, ss1576237080, ss1628432457, ss1671426490, ss1711326928, ss1807211324, ss1932817987, ss1967572523, ss2027159770, ss2155493166, ss2628059223, ss2699832674, ss2909620765, ss3009559100, ss3350028851, ss3676833887, ss3738953436, ss3750385648, ss3833083581, ss3878114815, ss3926721066, ss5205965802, ss5405152337, ss5510672787, ss5652999997, ss5837864432, ss5944357764, ss5981275014	NC_000012.11:40944101:A:T	NC_000012.12:40550299:A:T	(self)
75416622, 405087390, 89489299, 131131580, 8616565776, ss2189152793, ss3027388147, ss3693520271, ss3815714599, ss4915585923, ss5290536814, ss5485324113, ss5587890687, ss5755652195, ss5813229585, ss5850347553, ss5904084394	NC_000012.12:40550299:A:T	NC_000012.12:40550299:A:T	(self)
ss16151599	NT_029419.10:3087407:A:T	NC_000012.12:40550299:A:T	(self)
ss2319127, ss38892126	NT_029419.12:3087407:A:T	NC_000012.12:40550299:A: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 rs1492315

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

rs1492315