Name: rs12446989
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.

rs12446989

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:8571768 (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>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.088624 (23458/264690, TOPMED)
T=0.089100 (12484/140112, GnomAD)
T=0.05068 (1432/28258, 14KJPN) (+ 15 more)
T=0.10645 (2965/27854, ALFA)
T=0.04958 (831/16760, 8.3KJPN)
T=0.0824 (528/6404, 1000G_30x)
T=0.0861 (431/5008, 1000G)
T=0.1333 (597/4480, Estonian)
T=0.1235 (476/3854, ALSPAC)
T=0.1119 (415/3708, TWINSUK)
T=0.0468 (137/2930, KOREAN)
T=0.113 (113/998, GoNL)
T=0.112 (67/600, NorthernSweden)
T=0.088 (19/216, Qatari)
T=0.037 (8/216, Vietnamese)
C=0.474 (54/114, SGDP_PRJ)
T=0.10 (4/40, GENOME_DK)
C=0.45 (9/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TMEM114 : 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	27854	C=0.89355	A=0.00000, T=0.10645
European	Sub	22208	C=0.88225	A=0.00000, T=0.11775
African	Sub	3092	C=0.9757	A=0.0000, T=0.0243
African Others	Sub	124	C=0.992	A=0.000, T=0.008
African American	Sub	2968	C=0.9751	A=0.0000, T=0.0249
Asian	Sub	122	C=0.959	A=0.000, T=0.041
East Asian	Sub	96	C=0.96	A=0.00, T=0.04
Other Asian	Sub	26	C=0.96	A=0.00, T=0.04
Latin American 1	Sub	156	C=0.936	A=0.000, T=0.064
Latin American 2	Sub	676	C=0.840	A=0.000, T=0.160
South Asian	Sub	106	C=0.840	A=0.000, T=0.160
Other	Sub	1494	C=0.9096	A=0.0000, T=0.0904

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=0.911376	T=0.088624
gnomAD - Genomes	Global	Study-wide	140112	C=0.910900	T=0.089100
gnomAD - Genomes	European	Sub	75888	C=0.88089	T=0.11911
gnomAD - Genomes	African	Sub	41988	C=0.97194	T=0.02806
gnomAD - Genomes	American	Sub	13636	C=0.88024	T=0.11976
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.8949	T=0.1051
gnomAD - Genomes	East Asian	Sub	3132	C=0.9706	T=0.0294
gnomAD - Genomes	Other	Sub	2148	C=0.9101	T=0.0899
14KJPN	JAPANESE	Study-wide	28258	C=0.94932	T=0.05068
Allele Frequency Aggregator	Total	Global	27854	C=0.89355	A=0.00000, T=0.10645
Allele Frequency Aggregator	European	Sub	22208	C=0.88225	A=0.00000, T=0.11775
Allele Frequency Aggregator	African	Sub	3092	C=0.9757	A=0.0000, T=0.0243
Allele Frequency Aggregator	Other	Sub	1494	C=0.9096	A=0.0000, T=0.0904
Allele Frequency Aggregator	Latin American 2	Sub	676	C=0.840	A=0.000, T=0.160
Allele Frequency Aggregator	Latin American 1	Sub	156	C=0.936	A=0.000, T=0.064
Allele Frequency Aggregator	Asian	Sub	122	C=0.959	A=0.000, T=0.041
Allele Frequency Aggregator	South Asian	Sub	106	C=0.840	A=0.000, T=0.160
8.3KJPN	JAPANESE	Study-wide	16760	C=0.95042	T=0.04958
1000Genomes_30x	Global	Study-wide	6404	C=0.9176	T=0.0824
1000Genomes_30x	African	Sub	1786	C=0.9888	T=0.0112
1000Genomes_30x	Europe	Sub	1266	C=0.8705	T=0.1295
1000Genomes_30x	South Asian	Sub	1202	C=0.8453	T=0.1547
1000Genomes_30x	East Asian	Sub	1170	C=0.9675	T=0.0325
1000Genomes_30x	American	Sub	980	C=0.878	T=0.122
1000Genomes	Global	Study-wide	5008	C=0.9139	T=0.0861
1000Genomes	African	Sub	1322	C=0.9879	T=0.0121
1000Genomes	East Asian	Sub	1008	C=0.9643	T=0.0357
1000Genomes	Europe	Sub	1006	C=0.8648	T=0.1352
1000Genomes	South Asian	Sub	978	C=0.844	T=0.156
1000Genomes	American	Sub	694	C=0.870	T=0.130
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8667	T=0.1333
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8765	T=0.1235
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8881	T=0.1119
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.9532	T=0.0468
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.887	T=0.113
Northern Sweden	ACPOP	Study-wide	600	C=0.888	T=0.112
Qatari	Global	Study-wide	216	C=0.912	T=0.088
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.963	T=0.037
SGDP_PRJ	Global	Study-wide	114	C=0.474	T=0.526
The Danish reference pan genome	Danish	Study-wide	40	C=0.90	T=0.10
Siberian	Global	Study-wide	20	C=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 16	NC_000016.10:g.8571768C>A
GRCh38.p14 chr 16	NC_000016.10:g.8571768C>T
GRCh37.p13 chr 16	NC_000016.9:g.8621770C>A
GRCh37.p13 chr 16	NC_000016.9:g.8621770C>T
TMEM114 RefSeqGene	NG_041767.1:g.23426G>T
TMEM114 RefSeqGene	NG_041767.1:g.23426G>A

Gene: TMEM114, transmembrane protein 114 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TMEM114 transcript variant 1	NM_001146336.2:c.439+319G… NM_001146336.2:c.439+319G>T	N/A	Intron Variant
TMEM114 transcript variant 2	NM_001290095.2:c.302-1763… NM_001290095.2:c.302-1763G>T	N/A	Intron Variant
TMEM114 transcript variant 3	NM_001290097.2:c.196+319G… NM_001290097.2:c.196+319G>T	N/A	Intron Variant
TMEM114 transcript variant 4	NM_001290098.1:c.301+1744… NM_001290098.1:c.301+17445G>T	N/A	Intron Variant
TMEM114 transcript variant 5	NR_110736.2: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

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=	A	T
GRCh38.p14 chr 16	NC_000016.10:g.8571768=	NC_000016.10:g.8571768C>A	NC_000016.10:g.8571768C>T
GRCh37.p13 chr 16	NC_000016.9:g.8621770=	NC_000016.9:g.8621770C>A	NC_000016.9:g.8621770C>T
TMEM114 RefSeqGene	NG_041767.1:g.23426=	NG_041767.1:g.23426G>T	NG_041767.1:g.23426G>A
TMEM114 transcript variant 1	NM_001146336.1:c.138+319=	NM_001146336.1:c.138+319G>T	NM_001146336.1:c.138+319G>A
TMEM114 transcript variant 1	NM_001146336.2:c.439+319=	NM_001146336.2:c.439+319G>T	NM_001146336.2:c.439+319G>A
TMEM114 transcript variant 2	NM_001290095.2:c.302-1763=	NM_001290095.2:c.302-1763G>T	NM_001290095.2:c.302-1763G>A
TMEM114 transcript variant 3	NM_001290097.2:c.196+319=	NM_001290097.2:c.196+319G>T	NM_001290097.2:c.196+319G>A
TMEM114 transcript variant 4	NM_001290098.1:c.301+17445=	NM_001290098.1:c.301+17445G>T	NM_001290098.1:c.301+17445G>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#.

62 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss19346812	Feb 28, 2004 (120)
2	ABI	ss43493565	Mar 15, 2006 (126)
3	1000GENOMES	ss109179754	Jan 23, 2009 (130)
4	ENSEMBL	ss161818537	Dec 01, 2009 (131)
5	BUSHMAN	ss201420034	Jul 04, 2010 (132)
6	1000GENOMES	ss236947834	Jul 15, 2010 (132)
7	BL	ss255494051	May 09, 2011 (134)
8	ILLUMINA	ss483377818	May 04, 2012 (137)
9	ILLUMINA	ss483582218	May 04, 2012 (137)
10	ILLUMINA	ss535590703	Sep 08, 2015 (146)
11	TISHKOFF	ss564772053	Apr 25, 2013 (138)
12	SSMP	ss660517932	Apr 25, 2013 (138)
13	ILLUMINA	ss780254670	Sep 08, 2015 (146)
14	ILLUMINA	ss782132046	Sep 08, 2015 (146)
15	ILLUMINA	ss835740396	Sep 08, 2015 (146)
16	EVA-GONL	ss992268697	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1080475869	Aug 21, 2014 (142)
18	1000GENOMES	ss1355330361	Aug 21, 2014 (142)
19	DDI	ss1427774494	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1577829698	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1633982450	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1676976483	Apr 01, 2015 (144)
23	EVA_DECODE	ss1696304806	Apr 01, 2015 (144)
24	WEILL_CORNELL_DGM	ss1935682661	Feb 12, 2016 (147)
25	GENOMED	ss1968217308	Jul 19, 2016 (147)
26	JJLAB	ss2028627252	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2157038331	Dec 20, 2016 (150)
28	HUMAN_LONGEVITY	ss2210514695	Dec 20, 2016 (150)
29	ILLUMINA	ss2633292947	Nov 08, 2017 (151)
30	GRF	ss2701533607	Nov 08, 2017 (151)
31	GNOMAD	ss2940162415	Nov 08, 2017 (151)
32	SWEGEN	ss3014043295	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3028138711	Nov 08, 2017 (151)
34	CSHL	ss3351330481	Nov 08, 2017 (151)
35	ILLUMINA	ss3627475548	Oct 12, 2018 (152)
36	ILLUMINA	ss3631281269	Oct 12, 2018 (152)
37	ILLUMINA	ss3641068035	Oct 12, 2018 (152)
38	ILLUMINA	ss3641363502	Oct 12, 2018 (152)
39	ILLUMINA	ss3641943849	Oct 12, 2018 (152)
40	EGCUT_WGS	ss3681166775	Jul 13, 2019 (153)
41	EVA_DECODE	ss3698812703	Jul 13, 2019 (153)
42	ACPOP	ss3741324540	Jul 13, 2019 (153)
43	EVA	ss3753670314	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3818966490	Jul 13, 2019 (153)
45	EVA	ss3834468013	Apr 27, 2020 (154)
46	EVA	ss3840838660	Apr 27, 2020 (154)
47	EVA	ss3846329724	Apr 27, 2020 (154)
48	SGDP_PRJ	ss3883913251	Apr 27, 2020 (154)
49	KRGDB	ss3933204978	Apr 27, 2020 (154)
50	TOPMED	ss5007324361	Apr 26, 2021 (155)
51	TOMMO_GENOMICS	ss5218359739	Apr 26, 2021 (155)
52	1000G_HIGH_COVERAGE	ss5300086340	Oct 16, 2022 (156)
53	EVA	ss5422230318	Oct 16, 2022 (156)
54	HUGCELL_USP	ss5493619675	Oct 16, 2022 (156)
55	EVA	ss5511560082	Oct 16, 2022 (156)
56	1000G_HIGH_COVERAGE	ss5602293119	Oct 16, 2022 (156)
57	SANFORD_IMAGENETICS	ss5658436902	Oct 16, 2022 (156)
58	TOMMO_GENOMICS	ss5772820269	Oct 16, 2022 (156)
59	YY_MCH	ss5815746354	Oct 16, 2022 (156)
60	EVA	ss5846085692	Oct 16, 2022 (156)
61	EVA	ss5898232927	Oct 16, 2022 (156)
62	EVA	ss5949868170	Oct 16, 2022 (156)
63	1000Genomes	NC_000016.9 - 8621770	Oct 12, 2018 (152)
64	1000Genomes_30x	NC_000016.10 - 8571768	Oct 16, 2022 (156)
65	The Avon Longitudinal Study of Parents and Children	NC_000016.9 - 8621770	Oct 12, 2018 (152)
66	Genetic variation in the Estonian population	NC_000016.9 - 8621770	Oct 12, 2018 (152)
67	The Danish reference pan genome	NC_000016.9 - 8621770	Apr 27, 2020 (154)
68	gnomAD - Genomes	NC_000016.10 - 8571768	Apr 26, 2021 (155)
69	Genome of the Netherlands Release 5	NC_000016.9 - 8621770	Apr 27, 2020 (154)
70	KOREAN population from KRGDB	NC_000016.9 - 8621770	Apr 27, 2020 (154)
71	Northern Sweden	NC_000016.9 - 8621770	Jul 13, 2019 (153)
72	Qatari	NC_000016.9 - 8621770	Apr 27, 2020 (154)
73	SGDP_PRJ	NC_000016.9 - 8621770	Apr 27, 2020 (154)
74	Siberian	NC_000016.9 - 8621770	Apr 27, 2020 (154)
75	8.3KJPN	NC_000016.9 - 8621770	Apr 26, 2021 (155)
76	14KJPN	NC_000016.10 - 8571768	Oct 16, 2022 (156)
77	TopMed	NC_000016.10 - 8571768	Apr 26, 2021 (155)
78	UK 10K study - Twins	NC_000016.9 - 8621770	Oct 12, 2018 (152)
79	A Vietnamese Genetic Variation Database	NC_000016.9 - 8621770	Jul 13, 2019 (153)
80	ALFA	NC_000016.10 - 8571768	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
13548566166	NC_000016.10:8571767:C:A	NC_000016.10:8571767:C:A	(self)
ss109179754, ss201420034, ss255494051, ss483582218, ss1696304806	NC_000016.8:8561770:C:T	NC_000016.10:8571767:C:T	(self)
68463765, 38013961, 26905023, 4045545, 16957915, 40382372, 14609405, 17724583, 35930231, 9554685, 76329046, 38013961, 8448228, ss236947834, ss483377818, ss535590703, ss564772053, ss660517932, ss780254670, ss782132046, ss835740396, ss992268697, ss1080475869, ss1355330361, ss1427774494, ss1577829698, ss1633982450, ss1676976483, ss1935682661, ss1968217308, ss2028627252, ss2157038331, ss2633292947, ss2701533607, ss2940162415, ss3014043295, ss3351330481, ss3627475548, ss3631281269, ss3641068035, ss3641363502, ss3641943849, ss3681166775, ss3741324540, ss3753670314, ss3834468013, ss3840838660, ss3883913251, ss3933204978, ss5218359739, ss5422230318, ss5511560082, ss5658436902, ss5846085692, ss5949868170	NC_000016.9:8621769:C:T	NC_000016.10:8571767:C:T	(self)
89819054, 482449993, 106657373, 222870022, 13548566166, ss2210514695, ss3028138711, ss3698812703, ss3818966490, ss3846329724, ss5007324361, ss5300086340, ss5493619675, ss5602293119, ss5772820269, ss5815746354, ss5898232927	NC_000016.10:8571767:C:T	NC_000016.10:8571767:C:T	(self)
ss43493565, ss161818537	NT_010393.16:8561769:C:T	NC_000016.10:8571767:C:T	(self)
ss19346812	NT_010552.13:5962709:C:T	NC_000016.10:8571767: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 rs12446989

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

rs12446989