Name: rs117600412
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.

rs117600412

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:119655294 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.033522 (8873/264690, TOPMED)
C=0.031783 (4438/139636, GnomAD)
C=0.02037 (1603/78694, PAGE_STUDY) (+ 15 more)
C=0.00004 (1/28258, 14KJPN)
C=0.03769 (748/19848, ALFA)
C=0.0156 (100/6404, 1000G_30x)
C=0.0148 (74/5008, 1000G)
C=0.0312 (140/4480, Estonian)
C=0.0571 (220/3854, ALSPAC)
C=0.0585 (217/3708, TWINSUK)
C=0.062 (62/998, GoNL)
C=0.065 (39/600, NorthernSweden)
C=0.019 (4/216, Qatari)
C=0.03 (1/40, GENOME_DK)
T=0.50 (6/12, SGDP_PRJ)
C=0.50 (6/12, SGDP_PRJ)
T=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BAG3 : 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	19848	T=0.96231	C=0.03769
European	Sub	14364	T=0.95468	C=0.04532
African	Sub	3402	T=0.9897	C=0.0103
African Others	Sub	114	T=1.000	C=0.000
African American	Sub	3288	T=0.9894	C=0.0106
Asian	Sub	150	T=1.000	C=0.000
East Asian	Sub	122	T=1.000	C=0.000
Other Asian	Sub	28	T=1.00	C=0.00
Latin American 1	Sub	154	T=0.961	C=0.039
Latin American 2	Sub	616	T=0.969	C=0.031
South Asian	Sub	104	T=0.990	C=0.010
Other	Sub	1058	T=0.9660	C=0.0340

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	T=0.966478	C=0.033522
gnomAD - Genomes	Global	Study-wide	139636	T=0.968217	C=0.031783
gnomAD - Genomes	European	Sub	75664	T=0.95555	C=0.04445
gnomAD - Genomes	African	Sub	41808	T=0.99137	C=0.00863
gnomAD - Genomes	American	Sub	13594	T=0.96131	C=0.03869
gnomAD - Genomes	Ashkenazi Jewish	Sub	3312	T=0.9665	C=0.0335
gnomAD - Genomes	East Asian	Sub	3114	T=0.9997	C=0.0003
gnomAD - Genomes	Other	Sub	2144	T=0.9646	C=0.0354
The PAGE Study	Global	Study-wide	78694	T=0.97963	C=0.02037
The PAGE Study	AfricanAmerican	Sub	32512	T=0.98930	C=0.01070
The PAGE Study	Mexican	Sub	10810	T=0.97576	C=0.02424
The PAGE Study	Asian	Sub	8318	T=0.9999	C=0.0001
The PAGE Study	PuertoRican	Sub	7916	T=0.9394	C=0.0606
The PAGE Study	NativeHawaiian	Sub	4532	T=0.9861	C=0.0139
The PAGE Study	Cuban	Sub	4230	T=0.9518	C=0.0482
The PAGE Study	Dominican	Sub	3828	T=0.9801	C=0.0199
The PAGE Study	CentralAmerican	Sub	2450	T=0.9718	C=0.0282
The PAGE Study	SouthAmerican	Sub	1982	T=0.9758	C=0.0242
The PAGE Study	NativeAmerican	Sub	1260	T=0.9659	C=0.0341
The PAGE Study	SouthAsian	Sub	856	T=0.989	C=0.011
14KJPN	JAPANESE	Study-wide	28258	T=0.99996	C=0.00004
Allele Frequency Aggregator	Total	Global	19848	T=0.96231	C=0.03769
Allele Frequency Aggregator	European	Sub	14364	T=0.95468	C=0.04532
Allele Frequency Aggregator	African	Sub	3402	T=0.9897	C=0.0103
Allele Frequency Aggregator	Other	Sub	1058	T=0.9660	C=0.0340
Allele Frequency Aggregator	Latin American 2	Sub	616	T=0.969	C=0.031
Allele Frequency Aggregator	Latin American 1	Sub	154	T=0.961	C=0.039
Allele Frequency Aggregator	Asian	Sub	150	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	104	T=0.990	C=0.010
1000Genomes_30x	Global	Study-wide	6404	T=0.9844	C=0.0156
1000Genomes_30x	African	Sub	1786	T=0.9983	C=0.0017
1000Genomes_30x	Europe	Sub	1266	T=0.9676	C=0.0324
1000Genomes_30x	South Asian	Sub	1202	T=0.9884	C=0.0116
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	T=0.957	C=0.043
1000Genomes	Global	Study-wide	5008	T=0.9852	C=0.0148
1000Genomes	African	Sub	1322	T=0.9977	C=0.0023
1000Genomes	East Asian	Sub	1008	T=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	T=0.9672	C=0.0328
1000Genomes	South Asian	Sub	978	T=0.990	C=0.010
1000Genomes	American	Sub	694	T=0.960	C=0.040
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9688	C=0.0312
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9429	C=0.0571
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9415	C=0.0585
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.938	C=0.062
Northern Sweden	ACPOP	Study-wide	600	T=0.935	C=0.065
Qatari	Global	Study-wide	216	T=0.981	C=0.019
The Danish reference pan genome	Danish	Study-wide	40	T=0.97	C=0.03
SGDP_PRJ	Global	Study-wide	12	T=0.50	C=0.50
Siberian	Global	Study-wide	2	T=0.5	C=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 10	NC_000010.11:g.119655294T>C
GRCh37.p13 chr 10	NC_000010.10:g.121414806T>C
BAG3 RefSeqGene (LRG_742)	NG_016125.1:g.8925T>C

Gene: BAG3, BAG cochaperone 3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BAG3 transcript	NM_004281.4:c.180+3439T>C	N/A	Intron Variant
BAG3 transcript variant X1	XM_005270287.2:c.180+3439… XM_005270287.2:c.180+3439T>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	T=	C
GRCh38.p14 chr 10	NC_000010.11:g.119655294=	NC_000010.11:g.119655294T>C
GRCh37.p13 chr 10	NC_000010.10:g.121414806=	NC_000010.10:g.121414806T>C
BAG3 RefSeqGene (LRG_742)	NG_016125.1:g.8925=	NG_016125.1:g.8925T>C
BAG3 transcript	NM_004281.3:c.180+3439=	NM_004281.3:c.180+3439T>C
BAG3 transcript	NM_004281.4:c.180+3439=	NM_004281.4:c.180+3439T>C
BAG3 transcript variant X1	XM_005270287.1:c.180+3439=	XM_005270287.1:c.180+3439T>C
BAG3 transcript variant X1	XM_005270287.2:c.180+3439=	XM_005270287.2:c.180+3439T>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#.

37 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss235357704	Jul 15, 2010 (132)
2	ILLUMINA	ss533317498	Sep 08, 2015 (146)
3	EVA-GONL	ss987988416	Aug 21, 2014 (142)
4	1000GENOMES	ss1339321623	Aug 21, 2014 (142)
5	EVA_GENOME_DK	ss1575392945	Apr 01, 2015 (144)
6	EVA_DECODE	ss1597667469	Apr 01, 2015 (144)
7	EVA_UK10K_ALSPAC	ss1625574882	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1668568915	Apr 01, 2015 (144)
9	WEILL_CORNELL_DGM	ss1931345861	Feb 12, 2016 (147)
10	ILLUMINA	ss1959299883	Feb 12, 2016 (147)
11	JJLAB	ss2026409072	Sep 14, 2016 (149)
12	USC_VALOUEV	ss2154685909	Dec 20, 2016 (150)
13	HUMAN_LONGEVITY	ss2178612611	Dec 20, 2016 (150)
14	GNOMAD	ss2894118784	Nov 08, 2017 (151)
15	SWEGEN	ss3007251058	Nov 08, 2017 (151)
16	ILLUMINA	ss3021281318	Nov 08, 2017 (151)
17	CSHL	ss3349339673	Nov 08, 2017 (151)
18	ILLUMINA	ss3626548951	Oct 12, 2018 (152)
19	ILLUMINA	ss3651640917	Oct 12, 2018 (152)
20	EGCUT_WGS	ss3674669769	Jul 13, 2019 (153)
21	EVA_DECODE	ss3690808277	Jul 13, 2019 (153)
22	ILLUMINA	ss3725194354	Jul 13, 2019 (153)
23	ACPOP	ss3737734028	Jul 13, 2019 (153)
24	PAGE_CC	ss3771587485	Jul 13, 2019 (153)
25	EVA	ss3832364360	Apr 26, 2020 (154)
26	SGDP_PRJ	ss3875189203	Apr 26, 2020 (154)
27	TOPMED	ss4868735642	Apr 26, 2021 (155)
28	1000G_HIGH_COVERAGE	ss5285693058	Oct 16, 2022 (156)
29	EVA	ss5396455279	Oct 16, 2022 (156)
30	HUGCELL_USP	ss5481093535	Oct 16, 2022 (156)
31	EVA	ss5510191394	Oct 16, 2022 (156)
32	1000G_HIGH_COVERAGE	ss5580486242	Oct 16, 2022 (156)
33	SANFORD_IMAGENETICS	ss5650224753	Oct 16, 2022 (156)
34	TOMMO_GENOMICS	ss5746220107	Oct 16, 2022 (156)
35	EVA	ss5825046160	Oct 16, 2022 (156)
36	EVA	ss5880790943	Oct 16, 2022 (156)
37	EVA	ss5941531268	Oct 16, 2022 (156)
38	1000Genomes	NC_000010.10 - 121414806	Oct 12, 2018 (152)
39	1000Genomes_30x	NC_000010.11 - 119655294	Oct 16, 2022 (156)
40	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 121414806	Oct 12, 2018 (152)
41	Genetic variation in the Estonian population	NC_000010.10 - 121414806	Oct 12, 2018 (152)
42	The Danish reference pan genome	NC_000010.10 - 121414806	Apr 26, 2020 (154)
43	gnomAD - Genomes	NC_000010.11 - 119655294	Apr 26, 2021 (155)
44	Genome of the Netherlands Release 5	NC_000010.10 - 121414806	Apr 26, 2020 (154)
45	Northern Sweden	NC_000010.10 - 121414806	Jul 13, 2019 (153)
46	The PAGE Study	NC_000010.11 - 119655294	Jul 13, 2019 (153)
47	Qatari	NC_000010.10 - 121414806	Apr 26, 2020 (154)
48	SGDP_PRJ	NC_000010.10 - 121414806	Apr 26, 2020 (154)
49	Siberian	NC_000010.10 - 121414806	Apr 26, 2020 (154)
50	14KJPN	NC_000010.11 - 119655294	Oct 16, 2022 (156)
51	TopMed	NC_000010.11 - 119655294	Apr 26, 2021 (155)
52	UK 10K study - Twins	NC_000010.10 - 121414806	Oct 12, 2018 (152)
53	ALFA	NC_000010.11 - 119655294	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
ss1597667469	NC_000010.9:121404795:T:C	NC_000010.11:119655293:T:C	(self)
51777915, 28762332, 20408017, 2352499, 12818477, 11018893, 13387791, 27206183, 7202263, 28762332, ss235357704, ss533317498, ss987988416, ss1339321623, ss1575392945, ss1625574882, ss1668568915, ss1931345861, ss1959299883, ss2026409072, ss2154685909, ss2894118784, ss3007251058, ss3021281318, ss3349339673, ss3626548951, ss3651640917, ss3674669769, ss3737734028, ss3832364360, ss3875189203, ss5396455279, ss5510191394, ss5650224753, ss5825046160, ss5941531268	NC_000010.10:121414805:T:C	NC_000010.11:119655293:T:C	(self)
68012177, 365840069, 808954, 80057211, 84281297, 5977003674, ss2178612611, ss3690808277, ss3725194354, ss3771587485, ss4868735642, ss5285693058, ss5481093535, ss5580486242, ss5746220107, ss5880790943	NC_000010.11:119655293:T:C	NC_000010.11:119655293:T:C	(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 rs117600412

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

rs117600412