Name: rs116449213
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.

rs116449213

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:54434456 (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: T>A / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.030330 (8028/264690, TOPMED)
G=0.01079 (305/28258, 14KJPN)
G=0.00774 (141/18220, ALFA) (+ 16 more)
G=0.01068 (179/16760, 8.3KJPN)
G=0.0433 (277/6404, 1000G_30x)
G=0.0415 (208/5008, 1000G)
G=0.0045 (20/4480, Estonian)
G=0.0291 (112/3854, ALSPAC)
G=0.0291 (108/3708, TWINSUK)
G=0.0123 (36/2922, KOREAN)
G=0.021 (21/998, GoNL)
G=0.007 (4/600, NorthernSweden)
G=0.065 (14/216, Qatari)
G=0.019 (4/214, Vietnamese)
G=0.03 (1/40, GENOME_DK)
T=0.50 (13/26, SGDP_PRJ)
G=0.50 (13/26, SGDP_PRJ)
T=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TTYH1 : 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	18220	T=0.99226	A=0.00000, G=0.00774
European	Sub	13880	T=0.99229	A=0.00000, G=0.00771
African	Sub	2818	T=0.9897	A=0.0000, G=0.0103
African Others	Sub	112	T=0.991	A=0.000, G=0.009
African American	Sub	2706	T=0.9897	A=0.0000, G=0.0103
Asian	Sub	106	T=1.000	A=0.000, G=0.000
East Asian	Sub	84	T=1.00	A=0.00, G=0.00
Other Asian	Sub	22	T=1.00	A=0.00, G=0.00
Latin American 1	Sub	132	T=1.000	A=0.000, G=0.000
Latin American 2	Sub	552	T=1.000	A=0.000, G=0.000
South Asian	Sub	82	T=1.00	A=0.00, G=0.00
Other	Sub	650	T=0.992	A=0.000, G=0.008

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	T=0.969670	G=0.030330
14KJPN	JAPANESE	Study-wide	28258	T=0.98921	G=0.01079
Allele Frequency Aggregator	Total	Global	18220	T=0.99226	A=0.00000, G=0.00774
Allele Frequency Aggregator	European	Sub	13880	T=0.99229	A=0.00000, G=0.00771
Allele Frequency Aggregator	African	Sub	2818	T=0.9897	A=0.0000, G=0.0103
Allele Frequency Aggregator	Other	Sub	650	T=0.992	A=0.000, G=0.008
Allele Frequency Aggregator	Latin American 2	Sub	552	T=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	132	T=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	Asian	Sub	106	T=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	South Asian	Sub	82	T=1.00	A=0.00, G=0.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.98932	G=0.01068
1000Genomes_30x	Global	Study-wide	6404	T=0.9567	G=0.0433
1000Genomes_30x	African	Sub	1786	T=0.9681	G=0.0319
1000Genomes_30x	Europe	Sub	1266	T=0.9629	G=0.0371
1000Genomes_30x	South Asian	Sub	1202	T=0.9043	G=0.0957
1000Genomes_30x	East Asian	Sub	1170	T=0.9897	G=0.0103
1000Genomes_30x	American	Sub	980	T=0.953	G=0.047
1000Genomes	Global	Study-wide	5008	T=0.9585	G=0.0415
1000Genomes	African	Sub	1322	T=0.9682	G=0.0318
1000Genomes	East Asian	Sub	1008	T=0.9911	G=0.0089
1000Genomes	Europe	Sub	1006	T=0.9672	G=0.0328
1000Genomes	South Asian	Sub	978	T=0.905	G=0.095
1000Genomes	American	Sub	694	T=0.955	G=0.045
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9955	G=0.0045
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9709	G=0.0291
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9709	G=0.0291
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9877	G=0.0123
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.979	G=0.021
Northern Sweden	ACPOP	Study-wide	600	T=0.993	G=0.007
Qatari	Global	Study-wide	216	T=0.935	G=0.065
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.981	G=0.019
The Danish reference pan genome	Danish	Study-wide	40	T=0.97	G=0.03
SGDP_PRJ	Global	Study-wide	26	T=0.50	G=0.50
Siberian	Global	Study-wide	2	T=0.5	G=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 19	NC_000019.10:g.54434456T>A
GRCh38.p14 chr 19	NC_000019.10:g.54434456T>G
GRCh37.p13 chr 19 fix patch HG1079_PATCH	NW_004166865.1:g.408823T>A
GRCh37.p13 chr 19 fix patch HG1079_PATCH	NW_004166865.1:g.408823T>G
GRCh38.p14 chr 19 alt locus HSCHR19_4_CTG3_1	NT_187693.1:g.416750T>A
GRCh38.p14 chr 19 alt locus HSCHR19_4_CTG3_1	NT_187693.1:g.416750T>G
GRCh37.p13 chr 19	NC_000019.9:g.54945636T>A
GRCh37.p13 chr 19	NC_000019.9:g.54945636T>G
GRCh38.p14 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1	NW_003571060.1:g.339144T>A
GRCh38.p14 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1	NW_003571060.1:g.339144T>G
GRCh38.p14 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1	NW_003571054.1:g.340980T>A
GRCh38.p14 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1	NW_003571054.1:g.340980T>G

Gene: TTYH1, tweety family member 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TTYH1 transcript variant 2	NM_001005367.3:c.1126-108… NM_001005367.3:c.1126-1086T>A	N/A	Intron Variant
TTYH1 transcript variant 3	NM_001201461.2:c.1126-108… NM_001201461.2:c.1126-1086T>A	N/A	Intron Variant
TTYH1 transcript variant 1	NM_020659.4:c.1126-1086T>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	T=	A	G
GRCh38.p14 chr 19	NC_000019.10:g.54434456=	NC_000019.10:g.54434456T>A	NC_000019.10:g.54434456T>G
GRCh37.p13 chr 19 fix patch HG1079_PATCH	NW_004166865.1:g.408823=	NW_004166865.1:g.408823T>A	NW_004166865.1:g.408823T>G
GRCh38.p14 chr 19 alt locus HSCHR19_4_CTG3_1	NT_187693.1:g.416750=	NT_187693.1:g.416750T>A	NT_187693.1:g.416750T>G
GRCh37.p13 chr 19	NC_000019.9:g.54945636=	NC_000019.9:g.54945636T>A	NC_000019.9:g.54945636T>G
GRCh38.p14 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1	NW_003571060.1:g.339144=	NW_003571060.1:g.339144T>A	NW_003571060.1:g.339144T>G
GRCh38.p14 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1	NW_003571054.1:g.340980=	NW_003571054.1:g.340980T>A	NW_003571054.1:g.340980T>G
TTYH1 transcript variant 2	NM_001005367.2:c.1126-1086=	NM_001005367.2:c.1126-1086T>A	NM_001005367.2:c.1126-1086T>G
TTYH1 transcript variant 2	NM_001005367.3:c.1126-1086=	NM_001005367.3:c.1126-1086T>A	NM_001005367.3:c.1126-1086T>G
TTYH1 transcript variant 3	NM_001201461.1:c.1126-1086=	NM_001201461.1:c.1126-1086T>A	NM_001201461.1:c.1126-1086T>G
TTYH1 transcript variant 3	NM_001201461.2:c.1126-1086=	NM_001201461.2:c.1126-1086T>A	NM_001201461.2:c.1126-1086T>G
TTYH1 transcript variant 1	NM_020659.3:c.1126-1086=	NM_020659.3:c.1126-1086T>A	NM_020659.3:c.1126-1086T>G
TTYH1 transcript variant 1	NM_020659.4:c.1126-1086=	NM_020659.4:c.1126-1086T>A	NM_020659.4:c.1126-1086T>G
TTYH1 transcript variant X1	XM_005259091.1:c.1273-1086=	XM_005259091.1:c.1273-1086T>A	XM_005259091.1:c.1273-1086T>G
TTYH1 transcript variant X2	XM_005259092.1:c.1217-1086=	XM_005259092.1:c.1217-1086T>A	XM_005259092.1:c.1217-1086T>G
TTYH1 transcript variant X6	XM_005278285.1:c.1273-1086=	XM_005278285.1:c.1273-1086T>A	XM_005278285.1:c.1273-1086T>G
TTYH1 transcript variant X7	XM_005278286.1:c.1217-1086=	XM_005278286.1:c.1217-1086T>A	XM_005278286.1:c.1217-1086T>G

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#.

38 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss228193589	Jul 14, 2010 (132)
2	1000GENOMES	ss237717125	Jul 15, 2010 (132)
3	SSMP	ss661926992	Apr 25, 2013 (138)
4	EVA-GONL	ss994420094	Aug 21, 2014 (142)
5	JMKIDD_LAB	ss1081985622	Aug 21, 2014 (142)
6	1000GENOMES	ss1363628773	Aug 21, 2014 (142)
7	DDI	ss1428439498	Apr 01, 2015 (144)
8	EVA_GENOME_DK	ss1578686659	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1638184966	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1681178999	Apr 01, 2015 (144)
11	EVA_DECODE	ss1698473201	Apr 01, 2015 (144)
12	WEILL_CORNELL_DGM	ss1937925010	Feb 12, 2016 (147)
13	JJLAB	ss2029737589	Sep 14, 2016 (149)
14	USC_VALOUEV	ss2158288920	Dec 20, 2016 (150)
15	HUMAN_LONGEVITY	ss2226583434	Dec 20, 2016 (150)
16	SYSTEMSBIOZJU	ss2629366004	Nov 08, 2017 (151)
17	GRF	ss2702903789	Nov 08, 2017 (151)
18	GNOMAD	ss2964208280	Nov 08, 2017 (151)
19	SWEGEN	ss3017680296	Nov 08, 2017 (151)
20	EGCUT_WGS	ss3684403961	Jul 13, 2019 (153)
21	EVA_DECODE	ss3703007845	Jul 13, 2019 (153)
22	ACPOP	ss3743145727	Jul 13, 2019 (153)
23	EVA	ss3756203856	Jul 13, 2019 (153)
24	KHV_HUMAN_GENOMES	ss3821456015	Jul 13, 2019 (153)
25	SGDP_PRJ	ss3888485279	Apr 27, 2020 (154)
26	KRGDB	ss3938647019	Apr 27, 2020 (154)
27	TOPMED	ss5078610524	Apr 27, 2021 (155)
28	TOMMO_GENOMICS	ss5228333223	Apr 27, 2021 (155)
29	1000G_HIGH_COVERAGE	ss5307686248	Oct 13, 2022 (156)
30	EVA	ss5435562239	Oct 13, 2022 (156)
31	HUGCELL_USP	ss5500136042	Oct 13, 2022 (156)
32	1000G_HIGH_COVERAGE	ss5613590912	Oct 13, 2022 (156)
33	SANFORD_IMAGENETICS	ss5662637588	Oct 13, 2022 (156)
34	TOMMO_GENOMICS	ss5787158482	Oct 13, 2022 (156)
35	YY_MCH	ss5817710542	Oct 13, 2022 (156)
36	EVA	ss5840719074	Oct 13, 2022 (156)
37	EVA	ss5928554296	Oct 13, 2022 (156)
38	EVA	ss5954038478	Oct 13, 2022 (156)
39	1000Genomes	NC_000019.9 - 54945636	Oct 12, 2018 (152)
40	1000Genomes_30x	NC_000019.10 - 54434456	Oct 13, 2022 (156)
41	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 54945636	Oct 12, 2018 (152)
42	Genetic variation in the Estonian population	NC_000019.9 - 54945636	Oct 12, 2018 (152)
43	The Danish reference pan genome	NC_000019.9 - 54945636	Apr 27, 2020 (154)
44	gnomAD - Genomes Submission ignored due to conflicting rows: Row 543369228 (NC_000019.10:54434455:T:A 1/140164) Row 543369229 (NC_000019.10:54434455:T:G 3793/140156)	-	Apr 27, 2021 (155)
45	gnomAD - Genomes Submission ignored due to conflicting rows: Row 543369228 (NC_000019.10:54434455:T:A 1/140164) Row 543369229 (NC_000019.10:54434455:T:G 3793/140156)	-	Apr 27, 2021 (155)
46	Genome of the Netherlands Release 5	NC_000019.9 - 54945636	Apr 27, 2020 (154)
47	KOREAN population from KRGDB	NC_000019.9 - 54945636	Apr 27, 2020 (154)
48	Northern Sweden	NC_000019.9 - 54945636	Jul 13, 2019 (153)
49	Qatari	NC_000019.9 - 54945636	Apr 27, 2020 (154)
50	SGDP_PRJ	NC_000019.9 - 54945636	Apr 27, 2020 (154)
51	Siberian	NC_000019.9 - 54945636	Apr 27, 2020 (154)
52	8.3KJPN	NC_000019.9 - 54945636	Apr 27, 2021 (155)
53	14KJPN	NC_000019.10 - 54434456	Oct 13, 2022 (156)
54	TopMed	NC_000019.10 - 54434456	Apr 27, 2021 (155)
55	UK 10K study - Twins	NC_000019.9 - 54945636	Oct 12, 2018 (152)
56	A Vietnamese Genetic Variation Database	NC_000019.9 - 54945636	Jul 13, 2019 (153)
57	ALFA	NC_000019.10 - 54434456	Apr 27, 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).

Associated ID	History Updated (Build)
rs117241279	Aug 16, 2010 (132)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
3481166798	NC_000019.10:54434455:T:A	NC_000019.10:54434455:T:A	(self)
ss1698473201	NC_000019.8:59637447:T:G	NC_000019.10:54434455:T:G	(self)
77053128, 42653333, 30142209, 4867184, 19004065, 45824413, 16430592, 19966932, 40502259, 10805274, 86302530, 42653333, 9417217, ss228193589, ss237717125, ss661926992, ss994420094, ss1081985622, ss1363628773, ss1428439498, ss1578686659, ss1638184966, ss1681178999, ss1937925010, ss2029737589, ss2158288920, ss2629366004, ss2702903789, ss2964208280, ss3017680296, ss3684403961, ss3743145727, ss3756203856, ss3888485279, ss3938647019, ss5228333223, ss5435562239, ss5662637588, ss5840719074, ss5954038478	NC_000019.9:54945635:T:G	NC_000019.10:54434455:T:G	(self)
101116847, 120995586, 294156188, 3481166798, ss2226583434, ss3703007845, ss3821456015, ss5078610524, ss5307686248, ss5500136042, ss5613590912, ss5787158482, ss5817710542, ss5928554296	NC_000019.10:54434455:T:G	NC_000019.10:54434455:T:G	(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 rs116449213

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
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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

rs116449213