Name: rs796849079
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.

rs796849079

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:34229908-34229911 (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: delCT
Variation Type: Indel Insertion and Deletion
Frequency: delCT=0.121886 (32262/264690, TOPMED)
delCT=0.134110 (24658/183864, GnomAD_exome)
delCT=0.111170 (15568/140038, GnomAD) (+ 11 more)
delCT=0.17373 (8137/46838, ExAC)
delCT=0.23066 (6518/28258, 14KJPN)
delCT=0.10761 (2968/27582, ALFA)
delCT=0.22816 (3824/16760, 8.3KJPN)
delCT=0.1769 (886/5008, 1000G)
delCT=0.0766 (343/4480, Estonian)
delCT=0.2320 (425/1832, Korea1K)
delCT=0.104 (104/998, GoNL)
delCT=0.113 (68/600, NorthernSweden)
delCT=0.262 (56/214, Vietnamese)
delCT=0.07 (3/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: EMC4 : Non Coding Transcript Variant
SLC12A6 : 3 Prime UTR 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	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	27582	CTCT=0.89239	CT=0.10761	0.796389	0.011602	0.192009	0
European	Sub	20264	CTCT=0.90022	CT=0.09978	0.809416	0.008981	0.181603	1
African	Sub	3506	CTCT=0.8791	CT=0.1209	0.774672	0.016543	0.208785	0
African Others	Sub	122	CTCT=0.902	CT=0.098	0.803279	0.0	0.196721	0
African American	Sub	3384	CTCT=0.8783	CT=0.1217	0.773641	0.017139	0.20922	0
Asian	Sub	168	CTCT=0.744	CT=0.256	0.559524	0.071429	0.369048	0
East Asian	Sub	112	CTCT=0.768	CT=0.232	0.589286	0.053571	0.357143	0
Other Asian	Sub	56	CTCT=0.70	CT=0.30	0.5	0.107143	0.392857	0
Latin American 1	Sub	146	CTCT=0.774	CT=0.226	0.589041	0.041096	0.369863	0
Latin American 2	Sub	610	CTCT=0.856	CT=0.144	0.72459	0.013115	0.262295	1
South Asian	Sub	98	CTCT=0.86	CT=0.14	0.734694	0.020408	0.244898	32
Other	Sub	2790	CTCT=0.8767	CT=0.1233	0.772043	0.018638	0.209319	1

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	CTCT=0.878114	delCT=0.121886
gnomAD - Exomes	Global	Study-wide	183864	CTCT=0.865890	delCT=0.134110
gnomAD - Exomes	European	Sub	94440	CTCT=0.89923	delCT=0.10077
gnomAD - Exomes	Asian	Sub	38060	CTCT=0.78875	delCT=0.21125
gnomAD - Exomes	American	Sub	25280	CTCT=0.84308	delCT=0.15692
gnomAD - Exomes	African	Sub	12254	CTCT=0.87784	delCT=0.12216
gnomAD - Exomes	Ashkenazi Jewish	Sub	8910	CTCT=0.8927	delCT=0.1073
gnomAD - Exomes	Other	Sub	4920	CTCT=0.8616	delCT=0.1384
gnomAD - Genomes	Global	Study-wide	140038	CTCT=0.888830	delCT=0.111170
gnomAD - Genomes	European	Sub	75856	CTCT=0.90341	delCT=0.09659
gnomAD - Genomes	African	Sub	41964	CTCT=0.88135	delCT=0.11865
gnomAD - Genomes	American	Sub	13632	CTCT=0.87353	delCT=0.12647
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	CTCT=0.8857	delCT=0.1143
gnomAD - Genomes	East Asian	Sub	3112	CTCT=0.7192	delCT=0.2808
gnomAD - Genomes	Other	Sub	2150	CTCT=0.8679	delCT=0.1321
ExAC	Global	Study-wide	46838	CTCT=0.82627	delCT=0.17373
ExAC	Europe	Sub	25654	CTCT=0.85948	delCT=0.14052
ExAC	Asian	Sub	13048	CTCT=0.76334	delCT=0.23666
ExAC	African	Sub	5246	CTCT=0.8475	delCT=0.1525
ExAC	American	Sub	2440	CTCT=0.7676	delCT=0.2324
ExAC	Other	Sub	450	CTCT=0.829	delCT=0.171
14KJPN	JAPANESE	Study-wide	28258	CTCT=0.76934	delCT=0.23066
Allele Frequency Aggregator	Total	Global	27582	CTCT=0.89239	delCT=0.10761
Allele Frequency Aggregator	European	Sub	20264	CTCT=0.90022	delCT=0.09978
Allele Frequency Aggregator	African	Sub	3506	CTCT=0.8791	delCT=0.1209
Allele Frequency Aggregator	Other	Sub	2790	CTCT=0.8767	delCT=0.1233
Allele Frequency Aggregator	Latin American 2	Sub	610	CTCT=0.856	delCT=0.144
Allele Frequency Aggregator	Asian	Sub	168	CTCT=0.744	delCT=0.256
Allele Frequency Aggregator	Latin American 1	Sub	146	CTCT=0.774	delCT=0.226
Allele Frequency Aggregator	South Asian	Sub	98	CTCT=0.86	delCT=0.14
8.3KJPN	JAPANESE	Study-wide	16760	CTCT=0.77184	delCT=0.22816
1000Genomes	Global	Study-wide	5008	CTCT=0.8231	delCT=0.1769
1000Genomes	African	Sub	1322	CTCT=0.8691	delCT=0.1309
1000Genomes	East Asian	Sub	1008	CTCT=0.7242	delCT=0.2758
1000Genomes	Europe	Sub	1006	CTCT=0.8817	delCT=0.1183
1000Genomes	South Asian	Sub	978	CTCT=0.797	delCT=0.203
1000Genomes	American	Sub	694	CTCT=0.831	delCT=0.169
Genetic variation in the Estonian population	Estonian	Study-wide	4480	CTCT=0.9234	delCT=0.0766
Korean Genome Project	KOREAN	Study-wide	1832	CTCT=0.7680	delCT=0.2320
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	CTCT=0.896	delCT=0.104
Northern Sweden	ACPOP	Study-wide	600	CTCT=0.887	delCT=0.113
A Vietnamese Genetic Variation Database	Global	Study-wide	214	CTCT=0.738	delCT=0.262
The Danish reference pan genome	Danish	Study-wide	40	CTCT=0.93	delCT=0.07

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 15	NC_000015.10:g.34229908CT[1]
GRCh37.p13 chr 15	NC_000015.9:g.34522109CT[1]
SLC12A6 RefSeqGene (LRG_270)	NG_007951.1:g.113154AG[1]
EMC4 RefSeqGene	NG_054746.1:g.9912CT[1]

Gene: SLC12A6, solute carrier family 12 member 6 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC12A6 transcript variant 7	NM_001365088.1:c.3970_3… NM_001365088.1:c.3970_3973=	N/A	3 Prime UTR Variant
SLC12A6 transcript variant 5	NM_001042496.2:c.3970_3… NM_001042496.2:c.3970_3973=	N/A	3 Prime UTR Variant
SLC12A6 transcript variant 4	NM_001042495.2:c.3970_3… NM_001042495.2:c.3970_3973=	N/A	3 Prime UTR Variant
SLC12A6 transcript variant 3	NM_001042494.2:c.3970_3… NM_001042494.2:c.3970_3973=	N/A	3 Prime UTR Variant
SLC12A6 transcript variant 6	NM_001042497.2:c.3970_3… NM_001042497.2:c.3970_3973=	N/A	3 Prime UTR Variant
SLC12A6 transcript variant 1	NM_133647.2:c.3970_3973=	N/A	3 Prime UTR Variant
SLC12A6 transcript variant 2	NM_005135.2:c.	N/A	Genic Downstream Transcript Variant
SLC12A6 transcript variant X1	XM_006720793.5:c.3970_3… XM_006720793.5:c.3970_3973=	N/A	3 Prime UTR Variant
SLC12A6 transcript variant X2	XM_047433396.1:c.3970_3… XM_047433396.1:c.3970_3973=	N/A	3 Prime UTR Variant
SLC12A6 transcript variant X4	XM_011522269.4:c.	N/A	Genic Downstream Transcript Variant
SLC12A6 transcript variant X3	XR_931960.4:n.	N/A	Genic Downstream Transcript Variant

Gene: EMC4, ER membrane protein complex subunit 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EMC4 transcript variant 1	NM_016454.4:c.120_123=	N/A	3 Prime UTR Variant
EMC4 transcript variant 2	NM_001286420.2:c.61_64=	N/A	3 Prime UTR Variant
EMC4 transcript variant 3	NM_001351373.2:c.120_12… NM_001351373.2:c.120_123=	N/A	3 Prime UTR Variant
EMC4 transcript variant 4	NR_147140.2:n.618CT[1]	N/A	Non Coding Transcript 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	CTCT=	delCT
GRCh38.p14 chr 15	NC_000015.10:g.34229908_34229911=	NC_000015.10:g.34229908CT[1]
GRCh37.p13 chr 15	NC_000015.9:g.34522109_34522112=	NC_000015.9:g.34522109CT[1]
SLC12A6 RefSeqGene (LRG_270)	NG_007951.1:g.113154_113157=	NG_007951.1:g.113154AG[1]
SLC12A6 transcript variant 5	NM_001042496.2:c.3970_3973=	NM_001042496.2:c.*3970AG[1]
SLC12A6 transcript variant 3	NM_001042494.2:c.3970_3973=	NM_001042494.2:c.*3970AG[1]
SLC12A6 transcript variant 1	NM_133647.2:c.3970_3973=	NM_133647.2:c.*3970AG[1]
SLC12A6 transcript variant 6	NM_001042497.2:c.3970_3973=	NM_001042497.2:c.*3970AG[1]
SLC12A6 transcript variant 4	NM_001042495.2:c.3970_3973=	NM_001042495.2:c.*3970AG[1]
SLC12A6 transcript variant 7	NM_001365088.1:c.3970_3973=	NM_001365088.1:c.*3970AG[1]
EMC4 RefSeqGene	NG_054746.1:g.9912_9915=	NG_054746.1:g.9912CT[1]
EMC4 transcript variant 1	NM_016454.4:c.120_123=	NM_016454.4:c.*120CT[1]
EMC4 transcript variant 1	NM_016454.3:c.120_123=	NM_016454.3:c.*120CT[1]
EMC4 transcript	NM_016454.2:c.120_123=	NM_016454.2:c.*120CT[1]
EMC4 transcript variant 3	NM_001351373.2:c.120_123=	NM_001351373.2:c.*120CT[1]
EMC4 transcript variant 3	NM_001351373.1:c.120_123=	NM_001351373.1:c.*120CT[1]
EMC4 transcript variant 4	NR_147140.2:n.618_621=	NR_147140.2:n.618CT[1]
EMC4 transcript variant 4	NR_147140.1:n.637_640=	NR_147140.1:n.637CT[1]
EMC4 transcript variant 2	NM_001286420.2:c.61_64=	NM_001286420.2:c.*61CT[1]
EMC4 transcript variant 2	NM_001286420.1:c.61_64=	NM_001286420.1:c.*61CT[1]
SLC12A6 transcript variant X1	XM_006720793.5:c.3970_3973=	XM_006720793.5:c.*3970AG[1]
SLC12A6 transcript variant X2	XM_047433396.1:c.3970_3973=	XM_047433396.1:c.*3970AG[1]

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#.

47 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss289250497	Jan 10, 2018 (151)
2	1000GENOMES	ss327656515	Jan 10, 2018 (151)
3	1000GENOMES	ss327771838	Jan 10, 2018 (151)
4	1000GENOMES	ss328157726	Jan 10, 2018 (151)
5	1000GENOMES	ss498885702	Jan 10, 2018 (151)
6	LUNTER	ss552405824	Jan 10, 2018 (151)
7	LUNTER	ss552730865	Jan 10, 2018 (151)
8	LUNTER	ss553568712	Jan 10, 2018 (151)
9	TISHKOFF	ss554772465	Sep 08, 2015 (146)
10	SSMP	ss664265658	Jan 10, 2018 (151)
11	WARNICH_LAB	ss678404129	Jan 10, 2018 (151)
12	EVA-GONL	ss991663713	Jan 10, 2018 (151)
13	1000GENOMES	ss1374742060	Jan 10, 2018 (151)
14	EVA_GENOME_DK	ss1574842735	Jan 10, 2018 (151)
15	EVA_DECODE	ss1695674751	Jan 10, 2018 (151)
16	EVA_EXAC	ss1712072987	Jan 10, 2018 (151)
17	GENOMED	ss1968079457	Jan 10, 2018 (151)
18	JJLAB	ss2031258658	Jan 10, 2018 (151)
19	SYSTEMSBIOZJU	ss2628650029	Jan 10, 2018 (151)
20	GNOMAD	ss2749263892	Jan 10, 2018 (151)
21	GNOMAD	ss2933490040	Jan 10, 2018 (151)
22	SWEGEN	ss3013083267	Jan 10, 2018 (151)
23	MCHAISSO	ss3063814223	Jan 10, 2018 (151)
24	MCHAISSO	ss3065581597	Jan 10, 2018 (151)
25	BIOINF_KMB_FNS_UNIBA	ss3645375665	Oct 12, 2018 (152)
26	EGCUT_WGS	ss3680230842	Jul 13, 2019 (153)
27	EVA_DECODE	ss3697658769	Jul 13, 2019 (153)
28	ACPOP	ss3740822361	Jul 13, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3818254118	Jul 13, 2019 (153)
30	EVA	ss3834175686	Apr 27, 2020 (154)
31	KOGIC	ss3975895031	Apr 27, 2020 (154)
32	EVA	ss3986066675	Apr 26, 2021 (155)
33	EVA	ss3986641153	Apr 26, 2021 (155)
34	TOPMED	ss4987051352	Apr 26, 2021 (155)
35	TOMMO_GENOMICS	ss5215624051	Apr 26, 2021 (155)
36	EVA	ss5236922223	Apr 26, 2021 (155)
37	1000G_HIGH_COVERAGE	ss5298015426	Oct 16, 2022 (156)
38	HUGCELL_USP	ss5491791668	Oct 16, 2022 (156)
39	SANFORD_IMAGENETICS	ss5657267672	Oct 16, 2022 (156)
40	TOMMO_GENOMICS	ss5769259499	Oct 16, 2022 (156)
41	EVA	ss5800192105	Oct 16, 2022 (156)
42	YY_MCH	ss5815227804	Oct 16, 2022 (156)
43	EVA	ss5828039447	Oct 16, 2022 (156)
44	EVA	ss5848397600	Oct 16, 2022 (156)
45	EVA	ss5851242883	Oct 16, 2022 (156)
46	EVA	ss5875390184	Oct 16, 2022 (156)
47	EVA	ss5948662360	Oct 16, 2022 (156)
48	1000Genomes	NC_000015.9 - 34522109	Oct 12, 2018 (152)
49	Genetic variation in the Estonian population	NC_000015.9 - 34522109	Oct 12, 2018 (152)
50	ExAC	NC_000015.9 - 34522109	Oct 12, 2018 (152)
51	The Danish reference pan genome	NC_000015.9 - 34522109	Apr 27, 2020 (154)
52	gnomAD - Genomes	NC_000015.10 - 34229908	Apr 26, 2021 (155)
53	gnomAD - Exomes	NC_000015.9 - 34522109	Jul 13, 2019 (153)
54	Genome of the Netherlands Release 5	NC_000015.9 - 34522109	Apr 27, 2020 (154)
55	Korean Genome Project	NC_000015.10 - 34229908	Apr 27, 2020 (154)
56	Northern Sweden	NC_000015.9 - 34522109	Jul 13, 2019 (153)
57	8.3KJPN	NC_000015.9 - 34522109	Apr 26, 2021 (155)
58	14KJPN	NC_000015.10 - 34229908	Oct 16, 2022 (156)
59	TopMed	NC_000015.10 - 34229908	Apr 26, 2021 (155)
60	A Vietnamese Genetic Variation Database	NC_000015.9 - 34522109	Jul 13, 2019 (153)
61	ALFA	NC_000015.10 - 34229908	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
ss289250497, ss327656515, ss327771838, ss328157726, ss552405824, ss552730865, ss553568712, ss1695674751	NC_000015.8:32309400:CT:	NC_000015.10:34229907:CTCT:CT	(self)
66031455, 25969090, 2106855, 481549, 10367826, 16375822, 14107226, 73593358, 8155420, ss498885702, ss664265658, ss678404129, ss991663713, ss1374742060, ss1574842735, ss1712072987, ss1968079457, ss2031258658, ss2628650029, ss2749263892, ss2933490040, ss3013083267, ss3680230842, ss3740822361, ss3834175686, ss3986066675, ss3986641153, ss5215624051, ss5657267672, ss5800192105, ss5828039447, ss5948662360	NC_000015.9:34522108:CT:	NC_000015.10:34229907:CTCT:CT	(self)
ss554772465, ss5848397600	NC_000015.9:34522110:CT:	NC_000015.10:34229907:CTCT:CT	(self)
465468471, 32273032, 103096603, 202597012, ss3063814223, ss3065581597, ss3645375665, ss3697658769, ss3818254118, ss3975895031, ss4987051352, ss5236922223, ss5298015426, ss5491791668, ss5769259499, ss5815227804, ss5851242883, ss5875390184	NC_000015.10:34229907:CT:	NC_000015.10:34229907:CTCT:CT	(self)
8935865783	NC_000015.10:34229907:CTCT:CT	NC_000015.10:34229907:CTCT:CT	(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 rs796849079

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs796849079