Name: rs76228166
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.

rs76228166

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:15725191 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.009037 (2392/264690, TOPMED)
A=0.009398 (1318/140248, GnomAD)
A=0.19612 (5542/28258, 14KJPN) (+ 16 more)
A=0.00678 (128/18890, ALFA)
A=0.19499 (3268/16760, 8.3KJPN)
A=0.0340 (218/6404, 1000G_30x)
A=0.0367 (184/5008, 1000G)
A=0.0125 (56/4480, Estonian)
A=0.0034 (13/3854, ALSPAC)
A=0.0035 (13/3708, TWINSUK)
A=0.1713 (502/2930, KOREAN)
A=0.1616 (296/1832, Korea1K)
A=0.005 (5/998, GoNL)
A=0.022 (13/600, NorthernSweden)
A=0.151 (32/212, Vietnamese)
A=0.03 (1/40, GENOME_DK)
G=0.44 (15/34, SGDP_PRJ)
G=0.5 (4/8, Siberian)
A=0.5 (4/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BST1 : 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	18890	G=0.99322	A=0.00678
European	Sub	14286	G=0.99384	A=0.00616
African	Sub	2946	G=0.9983	A=0.0017
African Others	Sub	114	G=1.000	A=0.000
African American	Sub	2832	G=0.9982	A=0.0018
Asian	Sub	112	G=0.857	A=0.143
East Asian	Sub	86	G=0.86	A=0.14
Other Asian	Sub	26	G=0.85	A=0.15
Latin American 1	Sub	146	G=0.993	A=0.007
Latin American 2	Sub	610	G=0.990	A=0.010
South Asian	Sub	98	G=0.99	A=0.01
Other	Sub	692	G=0.984	A=0.016

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=0.990963	A=0.009037
gnomAD - Genomes	Global	Study-wide	140248	G=0.990602	A=0.009398
gnomAD - Genomes	European	Sub	75952	G=0.99106	A=0.00894
gnomAD - Genomes	African	Sub	42042	G=0.99864	A=0.00136
gnomAD - Genomes	American	Sub	13654	G=0.99634	A=0.00366
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.9979	A=0.0021
gnomAD - Genomes	East Asian	Sub	3128	G=0.8405	A=0.1595
gnomAD - Genomes	Other	Sub	2148	G=0.9879	A=0.0121
14KJPN	JAPANESE	Study-wide	28258	G=0.80388	A=0.19612
Allele Frequency Aggregator	Total	Global	18890	G=0.99322	A=0.00678
Allele Frequency Aggregator	European	Sub	14286	G=0.99384	A=0.00616
Allele Frequency Aggregator	African	Sub	2946	G=0.9983	A=0.0017
Allele Frequency Aggregator	Other	Sub	692	G=0.984	A=0.016
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.990	A=0.010
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.993	A=0.007
Allele Frequency Aggregator	Asian	Sub	112	G=0.857	A=0.143
Allele Frequency Aggregator	South Asian	Sub	98	G=0.99	A=0.01
8.3KJPN	JAPANESE	Study-wide	16760	G=0.80501	A=0.19499
1000Genomes_30x	Global	Study-wide	6404	G=0.9660	A=0.0340
1000Genomes_30x	African	Sub	1786	G=0.9989	A=0.0011
1000Genomes_30x	Europe	Sub	1266	G=0.9945	A=0.0055
1000Genomes_30x	South Asian	Sub	1202	G=0.9917	A=0.0083
1000Genomes_30x	East Asian	Sub	1170	G=0.8308	A=0.1692
1000Genomes_30x	American	Sub	980	G=0.999	A=0.001
1000Genomes	Global	Study-wide	5008	G=0.9633	A=0.0367
1000Genomes	African	Sub	1322	G=0.9992	A=0.0008
1000Genomes	East Asian	Sub	1008	G=0.8333	A=0.1667
1000Genomes	Europe	Sub	1006	G=0.9930	A=0.0070
1000Genomes	South Asian	Sub	978	G=0.993	A=0.007
1000Genomes	American	Sub	694	G=0.999	A=0.001
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9875	A=0.0125
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9966	A=0.0034
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9965	A=0.0035
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.8287	A=0.1713
Korean Genome Project	KOREAN	Study-wide	1832	G=0.8384	A=0.1616
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.995	A=0.005
Northern Sweden	ACPOP	Study-wide	600	G=0.978	A=0.022
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.849	A=0.151
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	A=0.03
SGDP_PRJ	Global	Study-wide	34	G=0.44	A=0.56
Siberian	Global	Study-wide	8	G=0.5	A=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 4	NC_000004.12:g.15725191G>A
GRCh37.p13 chr 4	NC_000004.11:g.15726814G>A

Gene: BST1, bone marrow stromal cell antigen 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BST1 transcript	NM_004334.3:c.851+2257G>A	N/A	Intron Variant
BST1 transcript variant X6	XM_005248186.3:c.851+2257… XM_005248186.3:c.851+2257G>A	N/A	Intron Variant
BST1 transcript variant X2	XM_011513878.4:c.851+2257… XM_011513878.4:c.851+2257G>A	N/A	Intron Variant
BST1 transcript variant X4	XM_011513879.3:c.851+2257… XM_011513879.3:c.851+2257G>A	N/A	Intron Variant
BST1 transcript variant X7	XM_011513881.3:c.677+2257… XM_011513881.3:c.677+2257G>A	N/A	Intron Variant
BST1 transcript variant X1	XM_017008565.3:c.851+2257… XM_017008565.3:c.851+2257G>A	N/A	Intron Variant
BST1 transcript variant X3	XM_017008566.3:c.851+2257… XM_017008566.3:c.851+2257G>A	N/A	Intron Variant
BST1 transcript variant X5	XM_005248185.3:c.	N/A	Genic Downstream Transcript 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
GRCh38.p14 chr 4	NC_000004.12:g.15725191=	NC_000004.12:g.15725191G>A
GRCh37.p13 chr 4	NC_000004.11:g.15726814=	NC_000004.11:g.15726814G>A
BST1 transcript	NM_004334.2:c.851+2257=	NM_004334.2:c.851+2257G>A
BST1 transcript	NM_004334.3:c.851+2257=	NM_004334.3:c.851+2257G>A
BST1 transcript variant X1	XM_005248184.1:c.851+2257=	XM_005248184.1:c.851+2257G>A
BST1 transcript variant X6	XM_005248186.1:c.851+2257=	XM_005248186.1:c.851+2257G>A
BST1 transcript variant X6	XM_005248186.3:c.851+2257=	XM_005248186.3:c.851+2257G>A
BST1 transcript variant X4	XM_005248187.1:c.677+2257=	XM_005248187.1:c.677+2257G>A
BST1 transcript variant X2	XM_011513878.4:c.851+2257=	XM_011513878.4:c.851+2257G>A
BST1 transcript variant X4	XM_011513879.3:c.851+2257=	XM_011513879.3:c.851+2257G>A
BST1 transcript variant X7	XM_011513881.3:c.677+2257=	XM_011513881.3:c.677+2257G>A
BST1 transcript variant X1	XM_017008565.3:c.851+2257=	XM_017008565.3:c.851+2257G>A
BST1 transcript variant X3	XM_017008566.3:c.851+2257=	XM_017008566.3:c.851+2257G>A

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#.

36 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss239592800	Jul 15, 2010 (132)
2	GMI	ss277590234	May 04, 2012 (137)
3	SSMP	ss651101526	Apr 25, 2013 (138)
4	EVA-GONL	ss979808455	Aug 21, 2014 (142)
5	JMKIDD_LAB	ss1071306295	Aug 21, 2014 (142)
6	1000GENOMES	ss1308593961	Aug 21, 2014 (142)
7	EVA_GENOME_DK	ss1580432283	Apr 01, 2015 (144)
8	EVA_DECODE	ss1589297082	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1609493068	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1652487101	Apr 01, 2015 (144)
11	USC_VALOUEV	ss2150206953	Dec 20, 2016 (150)
12	HUMAN_LONGEVITY	ss2260728707	Dec 20, 2016 (150)
13	SYSTEMSBIOZJU	ss2625549347	Nov 08, 2017 (151)
14	GRF	ss2705651098	Nov 08, 2017 (151)
15	GNOMAD	ss2806086903	Nov 08, 2017 (151)
16	SWEGEN	ss2994206943	Nov 08, 2017 (151)
17	EGCUT_WGS	ss3662114863	Jul 13, 2019 (153)
18	EVA_DECODE	ss3711486105	Jul 13, 2019 (153)
19	ACPOP	ss3730891991	Jul 13, 2019 (153)
20	EVA	ss3761448477	Jul 13, 2019 (153)
21	KHV_HUMAN_GENOMES	ss3804582305	Jul 13, 2019 (153)
22	SGDP_PRJ	ss3858308900	Apr 26, 2020 (154)
23	KRGDB	ss3904457631	Apr 26, 2020 (154)
24	KOGIC	ss3953606456	Apr 26, 2020 (154)
25	TOPMED	ss4604207845	Apr 26, 2021 (155)
26	TOMMO_GENOMICS	ss5164383190	Apr 26, 2021 (155)
27	1000G_HIGH_COVERAGE	ss5258187835	Oct 17, 2022 (156)
28	HUGCELL_USP	ss5457071312	Oct 17, 2022 (156)
29	1000G_HIGH_COVERAGE	ss5538696714	Oct 17, 2022 (156)
30	SANFORD_IMAGENETICS	ss5634432631	Oct 17, 2022 (156)
31	TOMMO_GENOMICS	ss5698083268	Oct 17, 2022 (156)
32	YY_MCH	ss5804794005	Oct 17, 2022 (156)
33	EVA	ss5843607829	Oct 17, 2022 (156)
34	EVA	ss5854096434	Oct 17, 2022 (156)
35	EVA	ss5862307328	Oct 17, 2022 (156)
36	EVA	ss5962810071	Oct 17, 2022 (156)
37	1000Genomes	NC_000004.11 - 15726814	Oct 12, 2018 (152)
38	1000Genomes_30x	NC_000004.12 - 15725191	Oct 17, 2022 (156)
39	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 15726814	Oct 12, 2018 (152)
40	Genetic variation in the Estonian population	NC_000004.11 - 15726814	Oct 12, 2018 (152)
41	The Danish reference pan genome	NC_000004.11 - 15726814	Apr 26, 2020 (154)
42	gnomAD - Genomes	NC_000004.12 - 15725191	Apr 26, 2021 (155)
43	Genome of the Netherlands Release 5	NC_000004.11 - 15726814	Apr 26, 2020 (154)
44	KOREAN population from KRGDB	NC_000004.11 - 15726814	Apr 26, 2020 (154)
45	Korean Genome Project	NC_000004.12 - 15725191	Apr 26, 2020 (154)
46	Northern Sweden	NC_000004.11 - 15726814	Jul 13, 2019 (153)
47	SGDP_PRJ	NC_000004.11 - 15726814	Apr 26, 2020 (154)
48	Siberian	NC_000004.11 - 15726814	Apr 26, 2020 (154)
49	8.3KJPN	NC_000004.11 - 15726814	Apr 26, 2021 (155)
50	14KJPN	NC_000004.12 - 15725191	Oct 17, 2022 (156)
51	TopMed	NC_000004.12 - 15725191	Apr 26, 2021 (155)
52	UK 10K study - Twins	NC_000004.11 - 15726814	Oct 12, 2018 (152)
53	A Vietnamese Genetic Variation Database	NC_000004.11 - 15726814	Jul 13, 2019 (153)
54	ALFA	NC_000004.12 - 15725191	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
ss277590234, ss1589297082	NC_000004.10:15335911:G:A	NC_000004.12:15725190:G:A	(self)
19947089, 11107898, 7853111, 6597222, 4888236, 11635025, 4176856, 10325880, 2723307, 22352497, 11107898, 2427598, ss239592800, ss651101526, ss979808455, ss1071306295, ss1308593961, ss1580432283, ss1609493068, ss1652487101, ss2150206953, ss2625549347, ss2705651098, ss2806086903, ss2994206943, ss3662114863, ss3730891991, ss3761448477, ss3858308900, ss3904457631, ss5164383190, ss5634432631, ss5843607829, ss5962810071	NC_000004.11:15726813:G:A	NC_000004.12:15725190:G:A	(self)
26222649, 141389553, 9984457, 31920372, 441585401, 11244568294, ss2260728707, ss3711486105, ss3804582305, ss3953606456, ss4604207845, ss5258187835, ss5457071312, ss5538696714, ss5698083268, ss5804794005, ss5854096434, ss5862307328	NC_000004.12:15725190:G:A	NC_000004.12:15725190:G:A	(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 rs76228166

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

rs76228166