Name: rs116497639
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.

rs116497639

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:30158760 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.027768 (7350/264690, TOPMED)
G=0.027494 (3854/140176, GnomAD)
G=0.00021 (6/28258, 14KJPN) (+ 16 more)
G=0.02537 (555/21876, ALFA)
G=0.00030 (5/16760, 8.3KJPN)
G=0.0309 (198/6404, 1000G_30x)
G=0.0304 (152/5008, 1000G)
G=0.0158 (71/4480, Estonian)
G=0.0091 (35/3854, ALSPAC)
G=0.0105 (39/3708, TWINSUK)
G=0.0140 (41/2922, KOREAN)
G=0.016 (16/998, GoNL)
G=0.003 (2/600, NorthernSweden)
G=0.002 (1/534, MGP)
G=0.037 (8/216, Qatari)
G=0.05 (2/40, GENOME_DK)
A=0.47 (19/40, SGDP_PRJ)
A=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TRIM10 : 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	21876	A=0.97463	G=0.02537
European	Sub	14286	A=0.98250	G=0.01750
African	Sub	5604	A=0.9559	G=0.0441
African Others	Sub	198	A=0.955	G=0.045
African American	Sub	5406	A=0.9560	G=0.0440
Asian	Sub	116	A=0.983	G=0.017
East Asian	Sub	88	A=1.00	G=0.00
Other Asian	Sub	28	A=0.93	G=0.07
Latin American 1	Sub	154	A=0.968	G=0.032
Latin American 2	Sub	616	A=0.964	G=0.036
South Asian	Sub	98	A=0.95	G=0.05
Other	Sub	1002	A=0.9760	G=0.0240

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=0.972232	G=0.027768
gnomAD - Genomes	Global	Study-wide	140176	A=0.972506	G=0.027494
gnomAD - Genomes	European	Sub	75918	A=0.98415	G=0.01585
gnomAD - Genomes	African	Sub	42006	A=0.95377	G=0.04623
gnomAD - Genomes	American	Sub	13656	A=0.95797	G=0.04203
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.9804	G=0.0196
gnomAD - Genomes	East Asian	Sub	3128	A=0.9974	G=0.0026
gnomAD - Genomes	Other	Sub	2148	A=0.9711	G=0.0289
14KJPN	JAPANESE	Study-wide	28258	A=0.99979	G=0.00021
Allele Frequency Aggregator	Total	Global	21876	A=0.97463	G=0.02537
Allele Frequency Aggregator	European	Sub	14286	A=0.98250	G=0.01750
Allele Frequency Aggregator	African	Sub	5604	A=0.9559	G=0.0441
Allele Frequency Aggregator	Other	Sub	1002	A=0.9760	G=0.0240
Allele Frequency Aggregator	Latin American 2	Sub	616	A=0.964	G=0.036
Allele Frequency Aggregator	Latin American 1	Sub	154	A=0.968	G=0.032
Allele Frequency Aggregator	Asian	Sub	116	A=0.983	G=0.017
Allele Frequency Aggregator	South Asian	Sub	98	A=0.95	G=0.05
8.3KJPN	JAPANESE	Study-wide	16760	A=0.99970	G=0.00030
1000Genomes_30x	Global	Study-wide	6404	A=0.9691	G=0.0309
1000Genomes_30x	African	Sub	1786	A=0.9423	G=0.0577
1000Genomes_30x	Europe	Sub	1266	A=0.9810	G=0.0190
1000Genomes_30x	South Asian	Sub	1202	A=0.9709	G=0.0291
1000Genomes_30x	East Asian	Sub	1170	A=0.9974	G=0.0026
1000Genomes_30x	American	Sub	980	A=0.966	G=0.034
1000Genomes	Global	Study-wide	5008	A=0.9696	G=0.0304
1000Genomes	African	Sub	1322	A=0.9402	G=0.0598
1000Genomes	East Asian	Sub	1008	A=0.9970	G=0.0030
1000Genomes	Europe	Sub	1006	A=0.9811	G=0.0189
1000Genomes	South Asian	Sub	978	A=0.971	G=0.029
1000Genomes	American	Sub	694	A=0.967	G=0.033
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9842	G=0.0158
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9909	G=0.0091
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9895	G=0.0105
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9860	G=0.0140
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.984	G=0.016
Northern Sweden	ACPOP	Study-wide	600	A=0.997	G=0.003
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	A=0.998	G=0.002
Qatari	Global	Study-wide	216	A=0.963	G=0.037
The Danish reference pan genome	Danish	Study-wide	40	A=0.95	G=0.05
SGDP_PRJ	Global	Study-wide	40	A=0.47	G=0.53
Siberian	Global	Study-wide	2	A=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 6	NC_000006.12:g.30158760A>G
GRCh37.p13 chr 6	NC_000006.11:g.30126537A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.1638566A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.1638672A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.1413888A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.1419484A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.1414676A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.1420261A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.1457687A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.1456985A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.1469481A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.1475101A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.1502837A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.1508422A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.2:g.1416855A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.1:g.1366771A>G

Gene: TRIM10, tripartite motif containing 10 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TRIM10 transcript variant 1	NM_006778.4:c.526-131T>C	N/A	Intron Variant
TRIM10 transcript variant 2	NM_052828.3:c.526-131T>C	N/A	Intron Variant
TRIM10 transcript variant X4	XM_011514221.2:c.580-131T… XM_011514221.2:c.580-131T>C	N/A	Intron Variant
TRIM10 transcript variant X1	XM_011514222.3:c.580-131T… XM_011514222.3:c.580-131T>C	N/A	Intron Variant
TRIM10 transcript variant X2	XM_011514223.3:c.580-131T… XM_011514223.3:c.580-131T>C	N/A	Intron Variant
TRIM10 transcript variant X5	XM_047418051.1:c.580-131T… XM_047418051.1:c.580-131T>C	N/A	Intron Variant
TRIM10 transcript variant X6	XM_047418052.1:c.580-131T… XM_047418052.1:c.580-131T>C	N/A	Intron Variant
TRIM10 transcript variant X3	XM_047418053.1:c.580-131T… XM_047418053.1:c.580-131T>C	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=	G
GRCh38.p14 chr 6	NC_000006.12:g.30158760=	NC_000006.12:g.30158760A>G
GRCh37.p13 chr 6	NC_000006.11:g.30126537=	NC_000006.11:g.30126537A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.1638566=	NT_113891.3:g.1638566A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.1638672=	NT_113891.2:g.1638672A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.1413888=	NT_167248.2:g.1413888A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.1419484=	NT_167248.1:g.1419484A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.1414676=	NT_167245.2:g.1414676A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.1420261=	NT_167245.1:g.1420261A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.2:g.1457687=	NT_167249.2:g.1457687A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1	NT_167249.1:g.1456985=	NT_167249.1:g.1456985A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.1469481=	NT_167246.2:g.1469481A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.1475101=	NT_167246.1:g.1475101A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.2:g.1502837=	NT_167247.2:g.1502837A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1	NT_167247.1:g.1508422=	NT_167247.1:g.1508422A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.2:g.1416855=	NT_167244.2:g.1416855A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1	NT_167244.1:g.1366771=	NT_167244.1:g.1366771A>G
TRIM10 transcript variant 1	NM_006778.3:c.526-131=	NM_006778.3:c.526-131T>C
TRIM10 transcript variant 1	NM_006778.4:c.526-131=	NM_006778.4:c.526-131T>C
TRIM10 transcript variant 2	NM_052828.2:c.526-131=	NM_052828.2:c.526-131T>C
TRIM10 transcript variant 2	NM_052828.3:c.526-131=	NM_052828.3:c.526-131T>C
TRIM10 transcript variant X4	XM_011514221.2:c.580-131=	XM_011514221.2:c.580-131T>C
TRIM10 transcript variant X1	XM_011514222.3:c.580-131=	XM_011514222.3:c.580-131T>C
TRIM10 transcript variant X2	XM_011514223.3:c.580-131=	XM_011514223.3:c.580-131T>C
TRIM10 transcript variant X5	XM_047418051.1:c.580-131=	XM_047418051.1:c.580-131T>C
TRIM10 transcript variant X6	XM_047418052.1:c.580-131=	XM_047418052.1:c.580-131T>C
TRIM10 transcript variant X3	XM_047418053.1:c.580-131=	XM_047418053.1:c.580-131T>C

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#.

41 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss222292040	Jul 14, 2010 (132)
2	ILLUMINA	ss535551869	Sep 08, 2015 (146)
3	TISHKOFF	ss559101808	Apr 25, 2013 (138)
4	SSMP	ss653018963	Apr 25, 2013 (138)
5	EVA-GONL	ss982744448	Aug 21, 2014 (142)
6	1000GENOMES	ss1319512312	Aug 21, 2014 (142)
7	EVA_GENOME_DK	ss1581596294	Apr 01, 2015 (144)
8	EVA_DECODE	ss1592291817	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1615251051	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1658245084	Apr 01, 2015 (144)
11	EVA_MGP	ss1711118866	Apr 01, 2015 (144)
12	WEILL_CORNELL_DGM	ss1925996636	Feb 12, 2016 (147)
13	JJLAB	ss2023626709	Sep 14, 2016 (149)
14	USC_VALOUEV	ss2151791988	Nov 08, 2017 (151)
15	HUMAN_LONGEVITY	ss2282872638	Dec 20, 2016 (150)
16	GNOMAD	ss2837313164	Nov 08, 2017 (151)
17	SWEGEN	ss2998765596	Nov 08, 2017 (151)
18	ILLUMINA	ss3629492479	Oct 12, 2018 (152)
19	EGCUT_WGS	ss3666688039	Jul 13, 2019 (153)
20	EVA_DECODE	ss3716875969	Jul 13, 2019 (153)
21	ACPOP	ss3733340482	Jul 13, 2019 (153)
22	EVA	ss3764799184	Jul 13, 2019 (153)
23	KHV_HUMAN_GENOMES	ss3807954752	Jul 13, 2019 (153)
24	EVA	ss3829817395	Apr 26, 2020 (154)
25	SGDP_PRJ	ss3864220223	Apr 26, 2020 (154)
26	KRGDB	ss3910994908	Apr 26, 2020 (154)
27	TOPMED	ss4698101685	Apr 26, 2021 (155)
28	TOMMO_GENOMICS	ss5176781856	Apr 26, 2021 (155)
29	1000G_HIGH_COVERAGE	ss5267893150	Oct 13, 2022 (156)
30	EVA	ss5364660807	Oct 13, 2022 (156)
31	HUGCELL_USP	ss5465634540	Oct 13, 2022 (156)
32	EVA	ss5508413362	Oct 13, 2022 (156)
33	1000G_HIGH_COVERAGE	ss5553536986	Oct 13, 2022 (156)
34	SANFORD_IMAGENETICS	ss5640057894	Oct 13, 2022 (156)
35	TOMMO_GENOMICS	ss5714621264	Oct 13, 2022 (156)
36	EVA	ss5800128380	Oct 13, 2022 (156)
37	YY_MCH	ss5807285672	Oct 13, 2022 (156)
38	EVA	ss5842000509	Oct 13, 2022 (156)
39	EVA	ss5848649417	Oct 13, 2022 (156)
40	EVA	ss5883200240	Oct 13, 2022 (156)
41	EVA	ss5968561277	Oct 13, 2022 (156)
42	1000Genomes	NC_000006.11 - 30126537	Oct 12, 2018 (152)
43	1000Genomes_30x	NC_000006.12 - 30158760	Oct 13, 2022 (156)
44	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 30126537	Oct 12, 2018 (152)
45	Genetic variation in the Estonian population	NC_000006.11 - 30126537	Oct 12, 2018 (152)
46	The Danish reference pan genome	NC_000006.11 - 30126537	Apr 26, 2020 (154)
47	gnomAD - Genomes	NC_000006.12 - 30158760	Apr 26, 2021 (155)
48	Genome of the Netherlands Release 5	NC_000006.11 - 30126537	Apr 26, 2020 (154)
49	KOREAN population from KRGDB	NC_000006.11 - 30126537	Apr 26, 2020 (154)
50	Medical Genome Project healthy controls from Spanish population	NC_000006.11 - 30126537	Apr 26, 2020 (154)
51	Northern Sweden	NC_000006.11 - 30126537	Jul 13, 2019 (153)
52	Qatari	NC_000006.11 - 30126537	Apr 26, 2020 (154)
53	SGDP_PRJ	NC_000006.11 - 30126537	Apr 26, 2020 (154)
54	Siberian	NC_000006.11 - 30126537	Apr 26, 2020 (154)
55	8.3KJPN	NC_000006.11 - 30126537	Apr 26, 2021 (155)
56	14KJPN	NC_000006.12 - 30158760	Oct 13, 2022 (156)
57	TopMed	NC_000006.12 - 30158760	Apr 26, 2021 (155)
58	UK 10K study - Twins	NC_000006.11 - 30126537	Oct 12, 2018 (152)
59	ALFA	NC_000006.12 - 30158760	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
ss1592291817	NC_000006.10:30234515:A:G	NC_000006.12:30158759:A:G	(self)
31277724, 17437485, 12426287, 7761233, 7744509, 18172302, 234626, 6625347, 8038566, 16237203, 4308342, 34751163, 17437485, ss222292040, ss535551869, ss559101808, ss653018963, ss982744448, ss1319512312, ss1581596294, ss1615251051, ss1658245084, ss1711118866, ss1925996636, ss2023626709, ss2151791988, ss2837313164, ss2998765596, ss3629492479, ss3666688039, ss3733340482, ss3764799184, ss3829817395, ss3864220223, ss3910994908, ss5176781856, ss5364660807, ss5508413362, ss5640057894, ss5800128380, ss5842000509, ss5848649417, ss5968561277	NC_000006.11:30126536:A:G	NC_000006.12:30158759:A:G	(self)
41062921, 220949990, 48458368, 535479243, 8364813326, ss2282872638, ss3716875969, ss3807954752, ss4698101685, ss5267893150, ss5465634540, ss5553536986, ss5714621264, ss5807285672, ss5883200240	NC_000006.12:30158759:A:G	NC_000006.12:30158759:A: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 rs116497639

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

rs116497639