Name: rs6839100
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.

rs6839100

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:76458036 (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: G>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.223250 (59092/264690, TOPMED)
A=0.03567 (1008/28258, 14KJPN)
A=0.03628 (608/16760, 8.3KJPN) (+ 16 more)
A=0.10346 (1449/14006, ALFA)
A=0.1907 (1221/6404, 1000G_30x)
A=0.1911 (957/5008, 1000G)
A=0.1837 (823/4480, Estonian)
A=0.2164 (834/3854, ALSPAC)
A=0.2209 (819/3708, TWINSUK)
A=0.0116 (34/2922, KOREAN)
A=0.0093 (17/1832, Korea1K)
A=0.220 (220/998, GoNL)
A=0.208 (125/600, NorthernSweden)
A=0.324 (70/216, Qatari)
A=0.019 (4/214, Vietnamese)
G=0.451 (64/142, SGDP_PRJ)
A=0.28 (11/40, GENOME_DK)
G=0.50 (7/14, Siberian)
A=0.50 (7/14, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SHROOM3 : 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	14006	G=0.89654	A=0.10346, T=0.00000
European	Sub	11154	G=0.87897	A=0.12103, T=0.00000
African	Sub	1610	G=0.9752	A=0.0248, T=0.0000
African Others	Sub	56	G=1.00	A=0.00, T=0.00
African American	Sub	1554	G=0.9743	A=0.0257, T=0.0000
Asian	Sub	108	G=1.000	A=0.000, T=0.000
East Asian	Sub	84	G=1.00	A=0.00, T=0.00
Other Asian	Sub	24	G=1.00	A=0.00, T=0.00
Latin American 1	Sub	84	G=1.00	A=0.00, T=0.00
Latin American 2	Sub	484	G=1.000	A=0.000, T=0.000
South Asian	Sub	62	G=0.97	A=0.03, T=0.00
Other	Sub	504	G=0.887	A=0.113, T=0.000

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	G=0.776750	A=0.223250
14KJPN	JAPANESE	Study-wide	28258	G=0.96433	A=0.03567
8.3KJPN	JAPANESE	Study-wide	16760	G=0.96372	A=0.03628
Allele Frequency Aggregator	Total	Global	14006	G=0.89654	A=0.10346, T=0.00000
Allele Frequency Aggregator	European	Sub	11154	G=0.87897	A=0.12103, T=0.00000
Allele Frequency Aggregator	African	Sub	1610	G=0.9752	A=0.0248, T=0.0000
Allele Frequency Aggregator	Other	Sub	504	G=0.887	A=0.113, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	484	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	108	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	84	G=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	62	G=0.97	A=0.03, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.8093	A=0.1907
1000Genomes_30x	African	Sub	1786	G=0.7060	A=0.2940
1000Genomes_30x	Europe	Sub	1266	G=0.7654	A=0.2346
1000Genomes_30x	South Asian	Sub	1202	G=0.7953	A=0.2047
1000Genomes_30x	East Asian	Sub	1170	G=0.9838	A=0.0162
1000Genomes_30x	American	Sub	980	G=0.863	A=0.137
1000Genomes	Global	Study-wide	5008	G=0.8089	A=0.1911
1000Genomes	African	Sub	1322	G=0.7110	A=0.2890
1000Genomes	East Asian	Sub	1008	G=0.9812	A=0.0188
1000Genomes	Europe	Sub	1006	G=0.7575	A=0.2425
1000Genomes	South Asian	Sub	978	G=0.786	A=0.214
1000Genomes	American	Sub	694	G=0.852	A=0.148
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8163	A=0.1837
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7836	A=0.2164
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7791	A=0.2209
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9884	A=0.0116
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9907	A=0.0093
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.780	A=0.220
Northern Sweden	ACPOP	Study-wide	600	G=0.792	A=0.208
Qatari	Global	Study-wide	216	G=0.676	A=0.324
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.981	A=0.019
SGDP_PRJ	Global	Study-wide	142	G=0.451	A=0.549
The Danish reference pan genome	Danish	Study-wide	40	G=0.72	A=0.28
Siberian	Global	Study-wide	14	G=0.50	A=0.50

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 4	NC_000004.12:g.76458036G>A
GRCh38.p14 chr 4	NC_000004.12:g.76458036G>T
GRCh37.p13 chr 4	NC_000004.11:g.77379189G>A
GRCh37.p13 chr 4	NC_000004.11:g.77379189G>T
SHROOM3 RefSeqGene	NG_028077.1:g.27937G>A
SHROOM3 RefSeqGene	NG_028077.1:g.27937G>T

Gene: SHROOM3, shroom family member 3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SHROOM3 transcript	NM_020859.4:c.168+21816G>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	G=	A	T
GRCh38.p14 chr 4	NC_000004.12:g.76458036=	NC_000004.12:g.76458036G>A	NC_000004.12:g.76458036G>T
GRCh37.p13 chr 4	NC_000004.11:g.77379189=	NC_000004.11:g.77379189G>A	NC_000004.11:g.77379189G>T
SHROOM3 RefSeqGene	NG_028077.1:g.27937=	NG_028077.1:g.27937G>A	NG_028077.1:g.27937G>T
SHROOM3 transcript	NM_020859.3:c.168+21816=	NM_020859.3:c.168+21816G>A	NM_020859.3:c.168+21816G>T
SHROOM3 transcript	NM_020859.4:c.168+21816=	NM_020859.4:c.168+21816G>A	NM_020859.4:c.168+21816G>T
SHROOM3 transcript variant X1	XM_005263162.1:c.168+21816=	XM_005263162.1:c.168+21816G>A	XM_005263162.1:c.168+21816G>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#.

47 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10153244	Jul 11, 2003 (116)
2	BCMHGSC_JDW	ss92650752	Mar 24, 2008 (129)
3	ENSEMBL	ss139706317	Dec 01, 2009 (131)
4	COMPLETE_GENOMICS	ss163627607	Jul 04, 2010 (132)
5	BL	ss253261704	May 09, 2011 (134)
6	PJP	ss293105819	May 09, 2011 (134)
7	1000GENOMES	ss331737982	May 09, 2011 (134)
8	TISHKOFF	ss557615462	Apr 25, 2013 (138)
9	SSMP	ss651424076	Apr 25, 2013 (138)
10	EVA-GONL	ss980277453	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1071661450	Aug 21, 2014 (142)
12	1000GENOMES	ss1310350748	Aug 21, 2014 (142)
13	DDI	ss1429933276	Apr 01, 2015 (144)
14	EVA_GENOME_DK	ss1580622398	Apr 01, 2015 (144)
15	EVA_DECODE	ss1589776776	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1610397949	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1653391982	Apr 01, 2015 (144)
18	WEILL_CORNELL_DGM	ss1923520569	Feb 12, 2016 (147)
19	JJLAB	ss2022345991	Sep 14, 2016 (149)
20	USC_VALOUEV	ss2150474538	Dec 20, 2016 (150)
21	HUMAN_LONGEVITY	ss2264099282	Dec 20, 2016 (150)
22	GNOMAD	ss2811043332	Nov 08, 2017 (151)
23	SWEGEN	ss2994950989	Nov 08, 2017 (151)
24	BIOINF_KMB_FNS_UNIBA	ss3024947699	Nov 08, 2017 (151)
25	CSHL	ss3345790149	Nov 08, 2017 (151)
26	EGCUT_WGS	ss3662834251	Jul 13, 2019 (153)
27	EVA_DECODE	ss3712347226	Jul 13, 2019 (153)
28	ACPOP	ss3731284904	Jul 13, 2019 (153)
29	EVA	ss3761981989	Jul 13, 2019 (153)
30	KHV_HUMAN_GENOMES	ss3805124274	Jul 13, 2019 (153)
31	EVA	ss3828621869	Apr 26, 2020 (154)
32	SGDP_PRJ	ss3859278357	Apr 26, 2020 (154)
33	KRGDB	ss3905536579	Apr 26, 2020 (154)
34	KOGIC	ss3954456968	Apr 26, 2020 (154)
35	TOPMED	ss4619088370	Apr 26, 2021 (155)
36	TOMMO_GENOMICS	ss5166387211	Apr 26, 2021 (155)
37	1000G_HIGH_COVERAGE	ss5259736587	Oct 13, 2022 (156)
38	EVA	ss5349970341	Oct 13, 2022 (156)
39	HUGCELL_USP	ss5458436936	Oct 13, 2022 (156)
40	EVA	ss5507578140	Oct 13, 2022 (156)
41	1000G_HIGH_COVERAGE	ss5541107834	Oct 13, 2022 (156)
42	SANFORD_IMAGENETICS	ss5635346216	Oct 13, 2022 (156)
43	TOMMO_GENOMICS	ss5700920445	Oct 13, 2022 (156)
44	YY_MCH	ss5805220199	Oct 13, 2022 (156)
45	EVA	ss5844204469	Oct 13, 2022 (156)
46	EVA	ss5864048214	Oct 13, 2022 (156)
47	EVA	ss5963724173	Oct 13, 2022 (156)
48	1000Genomes	NC_000004.11 - 77379189	Oct 12, 2018 (152)
49	1000Genomes_30x	NC_000004.12 - 76458036	Oct 13, 2022 (156)
50	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 77379189	Oct 12, 2018 (152)
51	Genetic variation in the Estonian population	NC_000004.11 - 77379189	Oct 12, 2018 (152)
52	The Danish reference pan genome	NC_000004.11 - 77379189	Apr 26, 2020 (154)
53	gnomAD - Genomes Submission ignored due to conflicting rows: Row 154198769 (NC_000004.12:76458035:G:A 32910/139910) Row 154198770 (NC_000004.12:76458035:G:T 3/139960)	-	Apr 26, 2021 (155)
54	gnomAD - Genomes Submission ignored due to conflicting rows: Row 154198769 (NC_000004.12:76458035:G:A 32910/139910) Row 154198770 (NC_000004.12:76458035:G:T 3/139960)	-	Apr 26, 2021 (155)
55	Genome of the Netherlands Release 5	NC_000004.11 - 77379189	Apr 26, 2020 (154)
56	KOREAN population from KRGDB	NC_000004.11 - 77379189	Apr 26, 2020 (154)
57	Korean Genome Project	NC_000004.12 - 76458036	Apr 26, 2020 (154)
58	Northern Sweden	NC_000004.11 - 77379189	Jul 13, 2019 (153)
59	Qatari	NC_000004.11 - 77379189	Apr 26, 2020 (154)
60	SGDP_PRJ	NC_000004.11 - 77379189	Apr 26, 2020 (154)
61	Siberian	NC_000004.11 - 77379189	Apr 26, 2020 (154)
62	8.3KJPN	NC_000004.11 - 77379189	Apr 26, 2021 (155)
63	14KJPN	NC_000004.12 - 76458036	Oct 13, 2022 (156)
64	TopMed	NC_000004.12 - 76458036	Apr 26, 2021 (155)
65	UK 10K study - Twins	NC_000004.11 - 77379189	Oct 12, 2018 (152)
66	A Vietnamese Genetic Variation Database	NC_000004.11 - 77379189	Jul 13, 2019 (153)
67	ALFA	NC_000004.12 - 76458036	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
ss92650752, ss163627607, ss253261704, ss293105819, ss1589776776	NC_000004.10:77598212:G:A	NC_000004.12:76458035:G:A	(self)
21768257, 12100935, 8572499, 6787337, 5345064, 12713973, 4569769, 5562499, 11295337, 2990892, 24356518, 12100935, 2665006, ss331737982, ss557615462, ss651424076, ss980277453, ss1071661450, ss1310350748, ss1429933276, ss1580622398, ss1610397949, ss1653391982, ss1923520569, ss2022345991, ss2150474538, ss2811043332, ss2994950989, ss3345790149, ss3662834251, ss3731284904, ss3761981989, ss3828621869, ss3859278357, ss3905536579, ss5166387211, ss5349970341, ss5507578140, ss5635346216, ss5844204469, ss5963724173	NC_000004.11:77379188:G:A	NC_000004.12:76458035:G:A	(self)
28633769, 10834969, 34757549, 456465926, 3445851296, ss2264099282, ss3024947699, ss3712347226, ss3805124274, ss3954456968, ss4619088370, ss5259736587, ss5458436936, ss5541107834, ss5700920445, ss5805220199, ss5864048214	NC_000004.12:76458035:G:A	NC_000004.12:76458035:G:A	(self)
ss10153244	NT_016354.15:1873893:G:A	NC_000004.12:76458035:G:A	(self)
ss139706317	NT_016354.19:1926909:G:A	NC_000004.12:76458035:G:A	(self)
ss2811043332	NC_000004.11:77379188:G:T	NC_000004.12:76458035:G:T	(self)
3445851296	NC_000004.12:76458035:G:T	NC_000004.12:76458035:G: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 rs6839100

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

rs6839100