Name: rs12978626
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.

rs12978626

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:2414934 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.135453 (35853/264690, TOPMED)
T=0.118664 (15967/134556, GnomAD)
T=0.41703 (11776/28238, 14KJPN) (+ 13 more)
T=0.08662 (1604/18518, ALFA)
T=0.41391 (6923/16726, 8.3KJPN)
T=0.1924 (1232/6404, 1000G_30x)
T=0.1957 (980/5008, 1000G)
T=0.0397 (178/4478, Estonian)
T=0.3975 (1164/2928, KOREAN)
T=0.3914 (717/1832, Korea1K)
T=0.046 (46/998, GoNL)
T=0.048 (29/598, NorthernSweden)
T=0.193 (58/300, HapMap)
T=0.069 (15/216, Qatari)
C=0.406 (73/180, SGDP_PRJ)
C=0.39 (7/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TMPRSS9 : 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	18518	C=0.91338	T=0.08662
European	Sub	14150	C=0.95336	T=0.04664
African	Sub	2898	C=0.7433	T=0.2567
African Others	Sub	114	C=0.684	T=0.316
African American	Sub	2784	C=0.7457	T=0.2543
Asian	Sub	112	C=0.598	T=0.402
East Asian	Sub	86	C=0.57	T=0.43
Other Asian	Sub	26	C=0.69	T=0.31
Latin American 1	Sub	146	C=0.911	T=0.089
Latin American 2	Sub	610	C=0.898	T=0.102
South Asian	Sub	98	C=0.89	T=0.11
Other	Sub	504	C=0.863	T=0.137

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=0.864547	T=0.135453
gnomAD - Genomes	Global	Study-wide	134556	C=0.881336	T=0.118664
gnomAD - Genomes	European	Sub	73876	C=0.95325	T=0.04675
gnomAD - Genomes	African	Sub	39178	C=0.74386	T=0.25614
gnomAD - Genomes	American	Sub	13054	C=0.91903	T=0.08097
gnomAD - Genomes	Ashkenazi Jewish	Sub	3306	C=0.9628	T=0.0372
gnomAD - Genomes	East Asian	Sub	3074	C=0.6448	T=0.3552
gnomAD - Genomes	Other	Sub	2068	C=0.9004	T=0.0996
14KJPN	JAPANESE	Study-wide	28238	C=0.58297	T=0.41703
Allele Frequency Aggregator	Total	Global	18518	C=0.91338	T=0.08662
Allele Frequency Aggregator	European	Sub	14150	C=0.95336	T=0.04664
Allele Frequency Aggregator	African	Sub	2898	C=0.7433	T=0.2567
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.898	T=0.102
Allele Frequency Aggregator	Other	Sub	504	C=0.863	T=0.137
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.911	T=0.089
Allele Frequency Aggregator	Asian	Sub	112	C=0.598	T=0.402
Allele Frequency Aggregator	South Asian	Sub	98	C=0.89	T=0.11
8.3KJPN	JAPANESE	Study-wide	16726	C=0.58609	T=0.41391
1000Genomes_30x	Global	Study-wide	6404	C=0.8076	T=0.1924
1000Genomes_30x	African	Sub	1786	C=0.7055	T=0.2945
1000Genomes_30x	Europe	Sub	1266	C=0.9518	T=0.0482
1000Genomes_30x	South Asian	Sub	1202	C=0.8594	T=0.1406
1000Genomes_30x	East Asian	Sub	1170	C=0.6650	T=0.3350
1000Genomes_30x	American	Sub	980	C=0.914	T=0.086
1000Genomes	Global	Study-wide	5008	C=0.8043	T=0.1957
1000Genomes	African	Sub	1322	C=0.7095	T=0.2905
1000Genomes	East Asian	Sub	1008	C=0.6577	T=0.3423
1000Genomes	Europe	Sub	1006	C=0.9503	T=0.0497
1000Genomes	South Asian	Sub	978	C=0.852	T=0.148
1000Genomes	American	Sub	694	C=0.919	T=0.081
Genetic variation in the Estonian population	Estonian	Study-wide	4478	C=0.9603	T=0.0397
KOREAN population from KRGDB	KOREAN	Study-wide	2928	C=0.6025	G=0.0000, T=0.3975
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6086	T=0.3914
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.954	T=0.046
Northern Sweden	ACPOP	Study-wide	598	C=0.952	T=0.048
HapMap	Global	Study-wide	300	C=0.807	T=0.193
HapMap	American	Sub	116	C=0.966	T=0.034
HapMap	African	Sub	108	C=0.778	T=0.222
HapMap	Asian	Sub	76	C=0.61	T=0.39
Qatari	Global	Study-wide	216	C=0.931	T=0.069
SGDP_PRJ	Global	Study-wide	180	C=0.406	T=0.594
Siberian	Global	Study-wide	18	C=0.39	T=0.61

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 19	NC_000019.10:g.2414934C>G
GRCh38.p14 chr 19	NC_000019.10:g.2414934C>T
GRCh37.p13 chr 19	NC_000019.9:g.2414932C>G
GRCh37.p13 chr 19	NC_000019.9:g.2414932C>T

Gene: TMPRSS9, transmembrane serine protease 9 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TMPRSS9 transcript variant 2	NM_001385642.1:c.878-736C… NM_001385642.1:c.878-736C>G	N/A	Intron Variant
TMPRSS9 transcript variant 5	NM_001395513.1:c.1574-736… NM_001395513.1:c.1574-736C>G	N/A	Intron Variant
TMPRSS9 transcript variant 1	NM_182973.3:c.1472-736C>G	N/A	Intron Variant
TMPRSS9 transcript variant 3	NR_169739.1:n.	N/A	Genic Downstream Transcript Variant
TMPRSS9 transcript variant 4	NR_169740.1:n.	N/A	Genic Downstream Transcript Variant
TMPRSS9 transcript variant X1	XM_011527978.3:c.1574-736… XM_011527978.3:c.1574-736C>G	N/A	Intron Variant
TMPRSS9 transcript variant X4	XM_011527980.1:c.365-736C… XM_011527980.1:c.365-736C>G	N/A	Intron Variant
TMPRSS9 transcript variant X2	XM_047438776.1:c.1541-736… XM_047438776.1:c.1541-736C>G	N/A	Intron Variant
TMPRSS9 transcript variant X3	XM_047438777.1:c.878-736C… XM_047438777.1:c.878-736C>G	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=	G	T
GRCh38.p14 chr 19	NC_000019.10:g.2414934=	NC_000019.10:g.2414934C>G	NC_000019.10:g.2414934C>T
GRCh37.p13 chr 19	NC_000019.9:g.2414932=	NC_000019.9:g.2414932C>G	NC_000019.9:g.2414932C>T
TMPRSS9 transcript variant 2	NM_001385642.1:c.878-736=	NM_001385642.1:c.878-736C>G	NM_001385642.1:c.878-736C>T
TMPRSS9 transcript variant 5	NM_001395513.1:c.1574-736=	NM_001395513.1:c.1574-736C>G	NM_001395513.1:c.1574-736C>T
TMPRSS9 transcript	NM_182973.1:c.1472-736=	NM_182973.1:c.1472-736C>G	NM_182973.1:c.1472-736C>T
TMPRSS9 transcript variant 1	NM_182973.3:c.1472-736=	NM_182973.3:c.1472-736C>G	NM_182973.3:c.1472-736C>T
TMPRSS9 transcript variant X1	XM_005259551.1:c.1574-736=	XM_005259551.1:c.1574-736C>G	XM_005259551.1:c.1574-736C>T
TMPRSS9 transcript variant X1	XM_011527978.3:c.1574-736=	XM_011527978.3:c.1574-736C>G	XM_011527978.3:c.1574-736C>T
TMPRSS9 transcript variant X4	XM_011527980.1:c.365-736=	XM_011527980.1:c.365-736C>G	XM_011527980.1:c.365-736C>T
TMPRSS9 transcript variant X2	XM_047438776.1:c.1541-736=	XM_047438776.1:c.1541-736C>G	XM_047438776.1:c.1541-736C>T
TMPRSS9 transcript variant X3	XM_047438777.1:c.878-736=	XM_047438777.1:c.878-736C>G	XM_047438777.1:c.878-736C>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#.

40 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss21531178	Apr 05, 2004 (121)
2	BGI	ss103418292	Dec 01, 2009 (131)
3	GMI	ss155530722	Dec 01, 2009 (131)
4	BUSHMAN	ss203592908	Jul 04, 2010 (132)
5	1000GENOMES	ss228010386	Jul 14, 2010 (132)
6	1000GENOMES	ss243806655	Jul 15, 2010 (132)
7	GMI	ss283099105	May 04, 2012 (137)
8	TISHKOFF	ss565811140	Apr 25, 2013 (138)
9	EVA-GONL	ss994017506	Aug 21, 2014 (142)
10	1000GENOMES	ss1362086408	Aug 21, 2014 (142)
11	HAMMER_LAB	ss1809175168	Sep 08, 2015 (146)
12	WEILL_CORNELL_DGM	ss1937494787	Feb 12, 2016 (147)
13	USC_VALOUEV	ss2158035580	Dec 20, 2016 (150)
14	HUMAN_LONGEVITY	ss2223753216	Dec 20, 2016 (150)
15	SYSTEMSBIOZJU	ss2629259935	Nov 08, 2017 (151)
16	GRF	ss2702639109	Nov 08, 2017 (151)
17	GNOMAD	ss2959673290	Nov 08, 2017 (151)
18	SWEGEN	ss3016971787	Nov 08, 2017 (151)
19	EGCUT_WGS	ss3683820047	Jul 13, 2019 (153)
20	EVA_DECODE	ss3702198345	Jul 13, 2019 (153)
21	ACPOP	ss3742792109	Jul 13, 2019 (153)
22	EVA	ss3755729634	Jul 13, 2019 (153)
23	KHV_HUMAN_GENOMES	ss3820982972	Jul 13, 2019 (153)
24	EVA	ss3835313304	Apr 27, 2020 (154)
25	SGDP_PRJ	ss3887606417	Apr 27, 2020 (154)
26	KRGDB	ss3937538269	Apr 27, 2020 (154)
27	KOGIC	ss3980664312	Apr 27, 2020 (154)
28	TOPMED	ss5065805235	Apr 26, 2021 (155)
29	TOMMO_GENOMICS	ss5226391363	Apr 26, 2021 (155)
30	1000G_HIGH_COVERAGE	ss5306236149	Oct 16, 2022 (156)
31	EVA	ss5433137809	Oct 16, 2022 (156)
32	EVA	ss5512028746	Oct 16, 2022 (156)
33	1000G_HIGH_COVERAGE	ss5611538126	Oct 16, 2022 (156)
34	SANFORD_IMAGENETICS	ss5661837547	Oct 16, 2022 (156)
35	TOMMO_GENOMICS	ss5784546784	Oct 16, 2022 (156)
36	YY_MCH	ss5817343471	Oct 16, 2022 (156)
37	EVA	ss5840156249	Oct 16, 2022 (156)
38	EVA	ss5852176448	Oct 16, 2022 (156)
39	EVA	ss5927032989	Oct 16, 2022 (156)
40	EVA	ss5953267953	Oct 16, 2022 (156)
41	1000Genomes	NC_000019.9 - 2414932	Oct 12, 2018 (152)
42	1000Genomes_30x	NC_000019.10 - 2414934	Oct 16, 2022 (156)
43	Genetic variation in the Estonian population	NC_000019.9 - 2414932	Oct 12, 2018 (152)
44	gnomAD - Genomes	NC_000019.10 - 2414934	Apr 26, 2021 (155)
45	Genome of the Netherlands Release 5	NC_000019.9 - 2414932	Apr 27, 2020 (154)
46	HapMap	NC_000019.10 - 2414934	Apr 27, 2020 (154)
47	KOREAN population from KRGDB	NC_000019.9 - 2414932	Apr 27, 2020 (154)
48	Korean Genome Project	NC_000019.10 - 2414934	Apr 27, 2020 (154)
49	Northern Sweden	NC_000019.9 - 2414932	Jul 13, 2019 (153)
50	Qatari	NC_000019.9 - 2414932	Apr 27, 2020 (154)
51	SGDP_PRJ	NC_000019.9 - 2414932	Apr 27, 2020 (154)
52	Siberian	NC_000019.9 - 2414932	Apr 27, 2020 (154)
53	8.3KJPN	NC_000019.9 - 2414932	Apr 26, 2021 (155)
54	14KJPN	NC_000019.10 - 2414934	Oct 16, 2022 (156)
55	TopMed	NC_000019.10 - 2414934	Apr 26, 2021 (155)
56	ALFA	NC_000019.10 - 2414934	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
44715663, ss3937538269	NC_000019.9:2414931:C:G	NC_000019.10:2414933:C:G	(self)
ss203592908, ss283099105	NC_000019.8:2365931:C:T	NC_000019.10:2414933:C:T	(self)
75453339, 29558295, 18632063, 44715663, 16076974, 19536709, 39623397, 10551934, 84360670, ss228010386, ss243806655, ss565811140, ss994017506, ss1362086408, ss1809175168, ss1937494787, ss2158035580, ss2629259935, ss2702639109, ss2959673290, ss3016971787, ss3683820047, ss3742792109, ss3755729634, ss3835313304, ss3887606417, ss3937538269, ss5226391363, ss5433137809, ss5512028746, ss5661837547, ss5840156249, ss5953267953	NC_000019.9:2414931:C:T	NC_000019.10:2414933:C:T	(self)
99064061, 532115357, 1659199, 37042313, 118383888, 281350899, 15048688816, ss2223753216, ss3702198345, ss3820982972, ss3980664312, ss5065805235, ss5306236149, ss5611538126, ss5784546784, ss5817343471, ss5852176448, ss5927032989	NC_000019.10:2414933:C:T	NC_000019.10:2414933:C:T	(self)
ss21531178, ss103418292, ss155530722	NT_011255.14:2354931:C:T	NC_000019.10:2414933: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 rs12978626

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

rs12978626