Name: rs6682857
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.

rs6682857

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:31063335 (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=0.009128 (2416/264690, TOPMED)
C=0.008400 (1178/140232, GnomAD)
C=0.01281 (362/28258, 14KJPN) (+ 13 more)
C=0.00582 (110/18890, ALFA)
C=0.01229 (206/16760, 8.3KJPN)
C=0.0123 (79/6404, 1000G_30x)
C=0.0128 (64/5008, 1000G)
C=0.0004 (2/4480, Estonian)
C=0.0047 (18/3854, ALSPAC)
C=0.0038 (14/3708, TWINSUK)
C=0.0075 (22/2922, KOREAN)
C=0.003 (3/998, GoNL)
C=0.009 (3/328, HapMap)
C=0.037 (8/214, Vietnamese)
T=0.50 (8/16, SGDP_PRJ)
C=0.50 (8/16, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PUM1 : 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	T=0.99418	C=0.00582
European	Sub	14286	T=0.99720	C=0.00280
African	Sub	2946	T=0.9840	C=0.0160
African Others	Sub	114	T=0.965	C=0.035
African American	Sub	2832	T=0.9848	C=0.0152
Asian	Sub	112	T=0.982	C=0.018
East Asian	Sub	86	T=1.00	C=0.00
Other Asian	Sub	26	T=0.92	C=0.08
Latin American 1	Sub	146	T=0.973	C=0.027
Latin American 2	Sub	610	T=0.992	C=0.008
South Asian	Sub	98	T=0.98	C=0.02
Other	Sub	692	T=0.986	C=0.014

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	T=0.990872	C=0.009128
gnomAD - Genomes	Global	Study-wide	140232	T=0.991600	C=0.008400
gnomAD - Genomes	European	Sub	75948	T=0.99609	C=0.00391
gnomAD - Genomes	African	Sub	42048	T=0.98302	C=0.01698
gnomAD - Genomes	American	Sub	13636	T=0.99391	C=0.00609
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.9976	C=0.0024
gnomAD - Genomes	East Asian	Sub	3132	T=0.9840	C=0.0160
gnomAD - Genomes	Other	Sub	2150	T=0.9879	C=0.0121
14KJPN	JAPANESE	Study-wide	28258	T=0.98719	C=0.01281
Allele Frequency Aggregator	Total	Global	18890	T=0.99418	C=0.00582
Allele Frequency Aggregator	European	Sub	14286	T=0.99720	C=0.00280
Allele Frequency Aggregator	African	Sub	2946	T=0.9840	C=0.0160
Allele Frequency Aggregator	Other	Sub	692	T=0.986	C=0.014
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.992	C=0.008
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.973	C=0.027
Allele Frequency Aggregator	Asian	Sub	112	T=0.982	C=0.018
Allele Frequency Aggregator	South Asian	Sub	98	T=0.98	C=0.02
8.3KJPN	JAPANESE	Study-wide	16760	T=0.98771	C=0.01229
1000Genomes_30x	Global	Study-wide	6404	T=0.9877	C=0.0123
1000Genomes_30x	African	Sub	1786	T=0.9838	C=0.0162
1000Genomes_30x	Europe	Sub	1266	T=0.9945	C=0.0055
1000Genomes_30x	South Asian	Sub	1202	T=0.9967	C=0.0033
1000Genomes_30x	East Asian	Sub	1170	T=0.9744	C=0.0256
1000Genomes_30x	American	Sub	980	T=0.991	C=0.009
1000Genomes	Global	Study-wide	5008	T=0.9872	C=0.0128
1000Genomes	African	Sub	1322	T=0.9826	C=0.0174
1000Genomes	East Asian	Sub	1008	T=0.9752	C=0.0248
1000Genomes	Europe	Sub	1006	T=0.9930	C=0.0070
1000Genomes	South Asian	Sub	978	T=0.997	C=0.003
1000Genomes	American	Sub	694	T=0.991	C=0.009
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9996	C=0.0004
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9953	C=0.0047
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9962	C=0.0038
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9925	C=0.0075
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.997	C=0.003
HapMap	Global	Study-wide	328	T=0.991	C=0.009
HapMap	African	Sub	120	T=0.992	C=0.008
HapMap	American	Sub	120	T=1.000	C=0.000
HapMap	Asian	Sub	88	T=0.98	C=0.02
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.963	C=0.037
SGDP_PRJ	Global	Study-wide	16	T=0.50	C=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 1	NC_000001.11:g.31063335T>C
GRCh37.p13 chr 1	NC_000001.10:g.31536182T>C

Gene: PUM1, pumilio RNA binding family member 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PUM1 transcript variant 1	NM_001020658.2:c.-12+2281… NM_001020658.2:c.-12+2281A>G	N/A	Intron Variant
PUM1 transcript variant 2	NM_014676.3:c.-12+2281A>G	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 1	NC_000001.11:g.31063335=	NC_000001.11:g.31063335T>C
GRCh37.p13 chr 1	NC_000001.10:g.31536182=	NC_000001.10:g.31536182T>C
PUM1 transcript variant 1	NM_001020658.1:c.-12+2281=	NM_001020658.1:c.-12+2281A>G
PUM1 transcript variant 1	NM_001020658.2:c.-12+2281=	NM_001020658.2:c.-12+2281A>G
PUM1 transcript variant 2	NM_014676.2:c.-12+2281=	NM_014676.2:c.-12+2281A>G
PUM1 transcript variant 2	NM_014676.3:c.-12+2281=	NM_014676.3:c.-12+2281A>G
PUM1 transcript variant X1	XM_005271357.1:c.97+2354=	XM_005271357.1:c.97+2354A>G
PUM1 transcript variant X2	XM_005271358.1:c.97+2354=	XM_005271358.1:c.97+2354A>G
PUM1 transcript variant X3	XM_005271359.1:c.97+2354=	XM_005271359.1:c.97+2354A>G
PUM1 transcript variant X4	XM_005271360.1:c.-12+2281=	XM_005271360.1:c.-12+2281A>G
PUM1 transcript variant X5	XM_005271361.1:c.97+2354=	XM_005271361.1:c.97+2354A>G
PUM1 transcript variant X6	XM_005271362.1:c.-12+2281=	XM_005271362.1:c.-12+2281A>G
PUM1 transcript variant X7	XM_005271363.1:c.-12+2281=	XM_005271363.1:c.-12+2281A>G
PUM1 transcript variant X8	XM_005271364.1:c.-12+2281=	XM_005271364.1:c.-12+2281A>G

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#.

32 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9862237	Jul 11, 2003 (116)
2	1000GENOMES	ss238184387	Jul 15, 2010 (132)
3	SSMP	ss647696789	Apr 25, 2013 (138)
4	EVA-GONL	ss975000189	Aug 21, 2014 (142)
5	JMKIDD_LAB	ss1067771412	Aug 21, 2014 (142)
6	1000GENOMES	ss1290248437	Aug 21, 2014 (142)
7	EVA_DECODE	ss1584359821	Apr 01, 2015 (144)
8	EVA_UK10K_ALSPAC	ss1599837347	Apr 01, 2015 (144)
9	EVA_UK10K_TWINSUK	ss1642831380	Apr 01, 2015 (144)
10	HUMAN_LONGEVITY	ss2161163399	Dec 20, 2016 (150)
11	GRF	ss2697532712	Nov 08, 2017 (151)
12	GNOMAD	ss2753291169	Nov 08, 2017 (151)
13	SWEGEN	ss2986555049	Nov 08, 2017 (151)
14	EGCUT_WGS	ss3654618287	Jul 12, 2019 (153)
15	EVA_DECODE	ss3686454222	Jul 12, 2019 (153)
16	EVA	ss3746004811	Jul 12, 2019 (153)
17	KHV_HUMAN_GENOMES	ss3799022943	Jul 12, 2019 (153)
18	SGDP_PRJ	ss3848520864	Apr 25, 2020 (154)
19	KRGDB	ss3893460490	Apr 25, 2020 (154)
20	TOPMED	ss4444000520	Apr 25, 2021 (155)
21	TOMMO_GENOMICS	ss5143188984	Apr 25, 2021 (155)
22	1000G_HIGH_COVERAGE	ss5241702185	Oct 13, 2022 (156)
23	EVA	ss5317687615	Oct 13, 2022 (156)
24	HUGCELL_USP	ss5442829476	Oct 13, 2022 (156)
25	1000G_HIGH_COVERAGE	ss5513700642	Oct 13, 2022 (156)
26	SANFORD_IMAGENETICS	ss5625217075	Oct 13, 2022 (156)
27	TOMMO_GENOMICS	ss5667716016	Oct 13, 2022 (156)
28	YY_MCH	ss5800457467	Oct 13, 2022 (156)
29	EVA	ss5831743827	Oct 13, 2022 (156)
30	EVA	ss5848843331	Oct 13, 2022 (156)
31	EVA	ss5907611178	Oct 13, 2022 (156)
32	EVA	ss5937034472	Oct 13, 2022 (156)
33	1000Genomes	NC_000001.10 - 31536182	Oct 11, 2018 (152)
34	1000Genomes_30x	NC_000001.11 - 31063335	Oct 13, 2022 (156)
35	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 31536182	Oct 11, 2018 (152)
36	Genetic variation in the Estonian population	NC_000001.10 - 31536182	Oct 11, 2018 (152)
37	gnomAD - Genomes	NC_000001.11 - 31063335	Apr 25, 2021 (155)
38	Genome of the Netherlands Release 5	NC_000001.10 - 31536182	Apr 25, 2020 (154)
39	HapMap	NC_000001.11 - 31063335	Apr 25, 2020 (154)
40	KOREAN population from KRGDB	NC_000001.10 - 31536182	Apr 25, 2020 (154)
41	SGDP_PRJ	NC_000001.10 - 31536182	Apr 25, 2020 (154)
42	8.3KJPN	NC_000001.10 - 31536182	Apr 25, 2021 (155)
43	14KJPN	NC_000001.11 - 31063335	Oct 13, 2022 (156)
44	TopMed	NC_000001.11 - 31063335	Apr 25, 2021 (155)
45	UK 10K study - Twins	NC_000001.10 - 31536182	Oct 11, 2018 (152)
46	A Vietnamese Genetic Variation Database	NC_000001.10 - 31536182	Jul 12, 2019 (153)
47	ALFA	NC_000001.11 - 31063335	Apr 25, 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
ss1584359821	NC_000001.9:31308768:T:C	NC_000001.11:31063334:T:C	(self)
943917, 505659, 356535, 217604, 637884, 537844, 1158291, 505659, 104457, ss238184387, ss647696789, ss975000189, ss1067771412, ss1290248437, ss1599837347, ss1642831380, ss2697532712, ss2753291169, ss2986555049, ss3654618287, ss3746004811, ss3848520864, ss3893460490, ss5143188984, ss5317687615, ss5625217075, ss5831743827, ss5937034472	NC_000001.10:31536181:T:C	NC_000001.11:31063334:T:C	(self)
1226577, 6633720, 39617, 1553120, 7606855, 1388345784, ss2161163399, ss3686454222, ss3799022943, ss4444000520, ss5241702185, ss5442829476, ss5513700642, ss5667716016, ss5800457467, ss5848843331, ss5907611178	NC_000001.11:31063334:T:C	NC_000001.11:31063334:T:C	(self)
ss9862237	NT_004511.15:1317766:T:C	NC_000001.11:31063334: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 rs6682857

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

rs6682857