Name: rs3928
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.

rs3928

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:15078350 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.232665 (61584/264690, TOPMED)
C=0.220880 (30948/140112, GnomAD)
C=0.25129 (7101/28258, 14KJPN) (+ 17 more)
C=0.24492 (4915/20068, ALFA)
C=0.25015 (4192/16758, 8.3KJPN)
C=0.2124 (1360/6404, 1000G_30x)
C=0.2039 (1021/5008, 1000G)
C=0.2469 (1106/4480, Estonian)
C=0.2714 (1046/3854, ALSPAC)
C=0.2888 (1071/3708, TWINSUK)
C=0.2474 (723/2922, KOREAN)
C=0.2598 (476/1832, Korea1K)
C=0.317 (316/998, GoNL)
C=0.257 (154/600, NorthernSweden)
C=0.198 (65/328, HapMap)
G=0.418 (97/232, SGDP_PRJ)
C=0.157 (34/216, Qatari)
C=0.098 (21/214, Vietnamese)
C=0.28 (11/40, GENOME_DK)
G=0.39 (7/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CALCB : 3 Prime UTR 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	20068	G=0.75508	C=0.24492
European	Sub	15436	G=0.72959	C=0.27041
African	Sub	2946	G=0.9131	C=0.0869
African Others	Sub	114	G=0.982	C=0.018
African American	Sub	2832	G=0.9103	C=0.0897
Asian	Sub	112	G=0.893	C=0.107
East Asian	Sub	86	G=0.87	C=0.13
Other Asian	Sub	26	G=0.96	C=0.04
Latin American 1	Sub	146	G=0.856	C=0.144
Latin American 2	Sub	610	G=0.582	C=0.418
South Asian	Sub	98	G=0.78	C=0.22
Other	Sub	720	G=0.757	C=0.243

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=0.767335	C=0.232665
gnomAD - Genomes	Global	Study-wide	140112	G=0.779120	C=0.220880
gnomAD - Genomes	European	Sub	75874	G=0.72967	C=0.27033
gnomAD - Genomes	African	Sub	41996	G=0.90944	C=0.09056
gnomAD - Genomes	American	Sub	13634	G=0.63210	C=0.36790
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.8026	C=0.1974
gnomAD - Genomes	East Asian	Sub	3134	G=0.8526	C=0.1474
gnomAD - Genomes	Other	Sub	2150	G=0.7674	C=0.2326
14KJPN	JAPANESE	Study-wide	28258	G=0.74871	C=0.25129
Allele Frequency Aggregator	Total	Global	20068	G=0.75508	C=0.24492
Allele Frequency Aggregator	European	Sub	15436	G=0.72959	C=0.27041
Allele Frequency Aggregator	African	Sub	2946	G=0.9131	C=0.0869
Allele Frequency Aggregator	Other	Sub	720	G=0.757	C=0.243
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.582	C=0.418
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.856	C=0.144
Allele Frequency Aggregator	Asian	Sub	112	G=0.893	C=0.107
Allele Frequency Aggregator	South Asian	Sub	98	G=0.78	C=0.22
8.3KJPN	JAPANESE	Study-wide	16758	G=0.74985	C=0.25015
1000Genomes_30x	Global	Study-wide	6404	G=0.7876	C=0.2124
1000Genomes_30x	African	Sub	1786	G=0.9328	C=0.0672
1000Genomes_30x	Europe	Sub	1266	G=0.7283	C=0.2717
1000Genomes_30x	South Asian	Sub	1202	G=0.7421	C=0.2579
1000Genomes_30x	East Asian	Sub	1170	G=0.8632	C=0.1368
1000Genomes_30x	American	Sub	980	G=0.565	C=0.435
1000Genomes	Global	Study-wide	5008	G=0.7961	C=0.2039
1000Genomes	African	Sub	1322	G=0.9357	C=0.0643
1000Genomes	East Asian	Sub	1008	G=0.8631	C=0.1369
1000Genomes	Europe	Sub	1006	G=0.7406	C=0.2594
1000Genomes	South Asian	Sub	978	G=0.746	C=0.254
1000Genomes	American	Sub	694	G=0.584	C=0.416
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7531	C=0.2469
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7286	C=0.2714
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7112	C=0.2888
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.7526	C=0.2474
Korean Genome Project	KOREAN	Study-wide	1832	G=0.7402	C=0.2598
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.683	C=0.317
Northern Sweden	ACPOP	Study-wide	600	G=0.743	C=0.257
HapMap	Global	Study-wide	328	G=0.802	C=0.198
HapMap	African	Sub	120	G=0.975	C=0.025
HapMap	American	Sub	118	G=0.669	C=0.331
HapMap	Asian	Sub	90	G=0.74	C=0.26
SGDP_PRJ	Global	Study-wide	232	G=0.418	C=0.582
Qatari	Global	Study-wide	216	G=0.843	C=0.157
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.902	C=0.098
The Danish reference pan genome	Danish	Study-wide	40	G=0.72	C=0.28
Siberian	Global	Study-wide	18	G=0.39	C=0.61

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 11	NC_000011.10:g.15078350G>C
GRCh37.p13 chr 11	NC_000011.9:g.15099896G>C

Gene: CALCB, calcitonin related polypeptide beta (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CALCB transcript	NM_000728.4:c.*293=	N/A	3 Prime UTR 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=	C
GRCh38.p14 chr 11	NC_000011.10:g.15078350=	NC_000011.10:g.15078350G>C
GRCh37.p13 chr 11	NC_000011.9:g.15099896=	NC_000011.9:g.15099896G>C
CALCB transcript	NM_000728.4:c.*293=	NM_000728.4:c.*293G>C
CALCB transcript	NM_000728.3:c.*293=	NM_000728.3:c.*293G>C
CALCB transcript variant X1	XM_005253135.1:c.*25+880=	XM_005253135.1:c.*25+880G>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#.

66 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SHGC/AFFYMETRIX	ss3965	Sep 19, 2000 (36)
2	SSAHASNP	ss20835915	Apr 05, 2004 (121)
3	PERLEGEN	ss24223992	Sep 20, 2004 (123)
4	SEQUENOM	ss24805814	Sep 20, 2004 (123)
5	ABI	ss38787898	Mar 14, 2006 (126)
6	ILLUMINA	ss65746767	Oct 16, 2006 (127)
7	HUMANGENOME_JCVI	ss97365542	Feb 05, 2009 (130)
8	KRIBB_YJKIM	ss104796536	Feb 05, 2009 (130)
9	ENSEMBL	ss142536962	Dec 01, 2009 (131)
10	GMI	ss155963218	Dec 01, 2009 (131)
11	ILLUMINA	ss160655771	Dec 01, 2009 (131)
12	BCM-HGSC-SUB	ss207699903	Jul 04, 2010 (132)
13	1000GENOMES	ss225107604	Jul 14, 2010 (132)
14	1000GENOMES	ss235458712	Jul 15, 2010 (132)
15	1000GENOMES	ss242109568	Jul 15, 2010 (132)
16	BL	ss254915880	May 09, 2011 (134)
17	GMI	ss280896569	May 04, 2012 (137)
18	PJP	ss291185171	May 09, 2011 (134)
19	ILLUMINA	ss481837738	Sep 08, 2015 (146)
20	SSMP	ss657812191	Apr 25, 2013 (138)
21	EVA-GONL	ss988240739	Aug 21, 2014 (142)
22	JMKIDD_LAB	ss1077524862	Aug 21, 2014 (142)
23	1000GENOMES	ss1340234413	Aug 21, 2014 (142)
24	EVA_GENOME_DK	ss1575542309	Apr 01, 2015 (144)
25	EVA_DECODE	ss1597918362	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1626053066	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1669047099	Apr 01, 2015 (144)
28	WEILL_CORNELL_DGM	ss1931602960	Feb 12, 2016 (147)
29	GENOMED	ss1967300092	Jul 19, 2016 (147)
30	JJLAB	ss2026545410	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2154832744	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2180427742	Dec 20, 2016 (150)
33	GRF	ss2699105412	Nov 08, 2017 (151)
34	GNOMAD	ss2896661496	Nov 08, 2017 (151)
35	SWEGEN	ss3007646364	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3027068393	Nov 08, 2017 (151)
37	CSHL	ss3349468455	Nov 08, 2017 (151)
38	ILLUMINA	ss3636126809	Oct 12, 2018 (152)
39	OMUKHERJEE_ADBS	ss3646422811	Oct 12, 2018 (152)
40	URBANLAB	ss3649541269	Oct 12, 2018 (152)
41	EGCUT_WGS	ss3675045089	Jul 13, 2019 (153)
42	EVA_DECODE	ss3691272843	Jul 13, 2019 (153)
43	ACPOP	ss3737947040	Jul 13, 2019 (153)
44	EVA	ss3748979352	Jul 13, 2019 (153)
45	KHV_HUMAN_GENOMES	ss3814327302	Jul 13, 2019 (153)
46	EVA	ss3832494825	Apr 26, 2020 (154)
47	EVA	ss3839794955	Apr 26, 2020 (154)
48	EVA	ss3845271570	Apr 26, 2020 (154)
49	SGDP_PRJ	ss3875707661	Apr 26, 2020 (154)
50	KRGDB	ss3923942752	Apr 26, 2020 (154)
51	KOGIC	ss3969265509	Apr 26, 2020 (154)
52	FSA-LAB	ss3983997483	Apr 26, 2021 (155)
53	TOPMED	ss4876217415	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5200813186	Apr 26, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5286504715	Oct 16, 2022 (156)
56	EVA	ss5397926488	Oct 16, 2022 (156)
57	HUGCELL_USP	ss5481796983	Oct 16, 2022 (156)
58	EVA	ss5510261323	Oct 16, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5581679225	Oct 16, 2022 (156)
60	SANFORD_IMAGENETICS	ss5650695633	Oct 16, 2022 (156)
61	TOMMO_GENOMICS	ss5747603912	Oct 16, 2022 (156)
62	YY_MCH	ss5812154339	Oct 16, 2022 (156)
63	EVA	ss5836303418	Oct 16, 2022 (156)
64	EVA	ss5849871174	Oct 16, 2022 (156)
65	EVA	ss5918947413	Oct 16, 2022 (156)
66	EVA	ss5942003340	Oct 16, 2022 (156)
67	1000Genomes	NC_000011.9 - 15099896	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000011.10 - 15078350	Oct 16, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 15099896	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000011.9 - 15099896	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000011.9 - 15099896	Apr 26, 2020 (154)
72	gnomAD - Genomes	NC_000011.10 - 15078350	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000011.9 - 15099896	Apr 26, 2020 (154)
74	HapMap	NC_000011.10 - 15078350	Apr 26, 2020 (154)
75	KOREAN population from KRGDB	NC_000011.9 - 15099896	Apr 26, 2020 (154)
76	Korean Genome Project	NC_000011.10 - 15078350	Apr 26, 2020 (154)
77	Northern Sweden	NC_000011.9 - 15099896	Jul 13, 2019 (153)
78	Qatari	NC_000011.9 - 15099896	Apr 26, 2020 (154)
79	SGDP_PRJ	NC_000011.9 - 15099896	Apr 26, 2020 (154)
80	Siberian	NC_000011.9 - 15099896	Apr 26, 2020 (154)
81	8.3KJPN	NC_000011.9 - 15099896	Apr 26, 2021 (155)
82	14KJPN	NC_000011.10 - 15078350	Oct 16, 2022 (156)
83	TopMed	NC_000011.10 - 15078350	Apr 26, 2021 (155)
84	UK 10K study - Twins	NC_000011.9 - 15099896	Oct 12, 2018 (152)
85	A Vietnamese Genetic Variation Database	NC_000011.9 - 15099896	Jul 13, 2019 (153)
86	ALFA	NC_000011.10 - 15078350	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).

Associated ID	History Updated (Build)
rs17299235	Oct 08, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss160655771, ss207699903, ss254915880, ss280896569, ss291185171, ss1597918362	NC_000011.8:15056471:G:C	NC_000011.10:15078349:G:C	(self)
52721396, 29285840, 20783337, 2456240, 13058917, 31120146, 11231905, 13644890, 27724641, 7349098, 58782493, 29285840, 6501478, ss225107604, ss235458712, ss242109568, ss481837738, ss657812191, ss988240739, ss1077524862, ss1340234413, ss1575542309, ss1626053066, ss1669047099, ss1931602960, ss1967300092, ss2026545410, ss2154832744, ss2699105412, ss2896661496, ss3007646364, ss3349468455, ss3636126809, ss3646422811, ss3675045089, ss3737947040, ss3748979352, ss3832494825, ss3839794955, ss3875707661, ss3923942752, ss3983997483, ss5200813186, ss5397926488, ss5510261323, ss5650695633, ss5836303418, ss5942003340	NC_000011.9:15099895:G:C	NC_000011.10:15078349:G:C	(self)
69205160, 372190594, 556174, 25643510, 81441016, 91763071, 2927672636, ss2180427742, ss3027068393, ss3649541269, ss3691272843, ss3814327302, ss3845271570, ss3969265509, ss4876217415, ss5286504715, ss5481796983, ss5581679225, ss5747603912, ss5812154339, ss5849871174, ss5918947413	NC_000011.10:15078349:G:C	NC_000011.10:15078349:G:C	(self)
ss20835915	NT_009237.16:13863835:G:C	NC_000011.10:15078349:G:C	(self)
ss3965, ss24223992, ss24805814, ss38787898, ss65746767, ss97365542, ss104796536, ss142536962, ss155963218	NT_009237.18:15039895:G:C	NC_000011.10:15078349:G: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 rs3928

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

rs3928