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dbSNP Short Genetic Variations

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.

rs760565

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3093753 (GRCh38.p13) 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
A>C / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.447501 (118449/264690, TOPMED)
A=0.450447 (63014/139892, GnomAD)
A=0.41265 (6916/16760, 8.3KJPN) (+ 13 more)
T=0.34662 (3801/10966, ALFA)
A=0.4171 (2089/5008, 1000G)
T=0.4301 (1927/4480, Estonian)
T=0.4224 (1628/3854, ALSPAC)
T=0.4369 (1620/3708, TWINSUK)
A=0.4658 (1364/2928, KOREAN)
A=0.4689 (859/1832, Korea1K)
T=0.448 (447/998, GoNL)
T=0.403 (242/600, NorthernSweden)
A=0.278 (119/428, SGDP_PRJ)
A=0.398 (86/216, Qatari)
A=0.41 (18/44, Siberian)
T=0.42 (17/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRDM16 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
Help

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.p13 chr 1 NC_000001.11:g.3093753A>C
GRCh38.p13 chr 1 NC_000001.11:g.3093753A>T
GRCh37.p13 chr 1 NC_000001.10:g.3010317A>C
GRCh37.p13 chr 1 NC_000001.10:g.3010317A>T
PRDM16 RefSeqGene NG_029576.2:g.29576A>C
PRDM16 RefSeqGene NG_029576.2:g.29576A>T
Gene: PRDM16, PR/SET domain 16 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PRDM16 transcript variant 1 NM_022114.4:c.37+24457A>C N/A Intron Variant
PRDM16 transcript variant 2 NM_199454.3:c.37+24457A>C N/A Intron Variant
Help

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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 10966 A=0.65338 C=0.00000, T=0.34662
European Sub 9604 A=0.6696 C=0.0000, T=0.3304
African Sub 728 A=0.291 C=0.000, T=0.709
African Others Sub 30 A=0.20 C=0.00, T=0.80
African American Sub 698 A=0.295 C=0.000, T=0.705
Asian Sub 20 A=0.90 C=0.00, T=0.10
East Asian Sub 14 A=0.93 C=0.00, T=0.07
Other Asian Sub 6 A=0.8 C=0.0, T=0.2
Latin American 1 Sub 28 A=1.00 C=0.00, T=0.00
Latin American 2 Sub 226 A=1.000 C=0.000, T=0.000
South Asian Sub 30 A=0.93 C=0.00, T=0.07
Other Sub 330 A=0.673 C=0.000, T=0.327


Help

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 A=0.447501 T=0.552499
gnomAD - Genomes Global Study-wide 139892 A=0.450447 T=0.549553
gnomAD - Genomes European Sub 75774 A=0.56403 T=0.43597
gnomAD - Genomes African Sub 41908 A=0.20287 T=0.79713
gnomAD - Genomes American Sub 13644 A=0.55453 T=0.44547
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.5482 T=0.4518
gnomAD - Genomes East Asian Sub 3096 A=0.4532 T=0.5468
gnomAD - Genomes Other Sub 2150 A=0.4577 T=0.5423
8.3KJPN JAPANESE Study-wide 16760 A=0.41265 T=0.58735
1000Genomes Global Study-wide 5008 A=0.4171 T=0.5829
1000Genomes African Sub 1322 A=0.1399 T=0.8601
1000Genomes East Asian Sub 1008 A=0.4494 T=0.5506
1000Genomes Europe Sub 1006 A=0.5517 T=0.4483
1000Genomes South Asian Sub 978 A=0.497 T=0.503
1000Genomes American Sub 694 A=0.591 T=0.409
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.5699 T=0.4301
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.5776 T=0.4224
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.5631 T=0.4369
KOREAN population from KRGDB KOREAN Study-wide 2928 A=0.4658 T=0.5342
Korean Genome Project KOREAN Study-wide 1832 A=0.4689 T=0.5311
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.552 T=0.448
Northern Sweden ACPOP Study-wide 600 A=0.597 T=0.403
SGDP_PRJ Global Study-wide 428 A=0.278 T=0.722
Qatari Global Study-wide 216 A=0.398 T=0.602
Siberian Global Study-wide 44 A=0.41 T=0.59
The Danish reference pan genome Danish Study-wide 40 A=0.57 T=0.42
Help

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 A= C T
GRCh38.p13 chr 1 NC_000001.11:g.3093753= NC_000001.11:g.3093753A>C NC_000001.11:g.3093753A>T
GRCh37.p13 chr 1 NC_000001.10:g.3010317= NC_000001.10:g.3010317A>C NC_000001.10:g.3010317A>T
PRDM16 RefSeqGene NG_029576.2:g.29576= NG_029576.2:g.29576A>C NG_029576.2:g.29576A>T
PRDM16 transcript variant 1 NM_022114.3:c.37+24457= NM_022114.3:c.37+24457A>C NM_022114.3:c.37+24457A>T
PRDM16 transcript variant 1 NM_022114.4:c.37+24457= NM_022114.4:c.37+24457A>C NM_022114.4:c.37+24457A>T
PRDM16 transcript variant 2 NM_199454.2:c.37+24457= NM_199454.2:c.37+24457A>C NM_199454.2:c.37+24457A>T
PRDM16 transcript variant 2 NM_199454.3:c.37+24457= NM_199454.3:c.37+24457A>C NM_199454.3:c.37+24457A>T
PRDM16 transcript variant X1 XM_005244772.1:c.37+24457= XM_005244772.1:c.37+24457A>C XM_005244772.1:c.37+24457A>T
PRDM16 transcript variant X2 XM_005244773.1:c.37+24457= XM_005244773.1:c.37+24457A>C XM_005244773.1:c.37+24457A>T
PRDM16 transcript variant X3 XM_005244774.1:c.37+24457= XM_005244774.1:c.37+24457A>C XM_005244774.1:c.37+24457A>T
Help

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#.

67 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss133530 Oct 05, 2000 (86)
2 SC_JCM ss4214182 Nov 05, 2001 (101)
3 WI_SSAHASNP ss6396355 Feb 20, 2003 (111)
4 WI_SSAHASNP ss11346288 Jul 11, 2003 (116)
5 CSHL-HAPMAP ss17353135 Feb 27, 2004 (120)
6 SSAHASNP ss20452604 Apr 05, 2004 (121)
7 ABI ss44112850 Mar 14, 2006 (126)
8 HGSV ss78321732 Dec 06, 2007 (129)
9 HGSV ss82796670 Dec 15, 2007 (130)
10 HGSV ss83467748 Dec 15, 2007 (130)
11 HUMANGENOME_JCVI ss99180725 Feb 05, 2009 (130)
12 BGI ss105114176 Dec 01, 2009 (131)
13 1000GENOMES ss107944806 Jan 22, 2009 (130)
14 1000GENOMES ss109958776 Jan 24, 2009 (130)
15 ILLUMINA-UK ss118447888 Feb 14, 2009 (130)
16 ENSEMBL ss138984798 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss162998158 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss163728895 Jul 04, 2010 (132)
19 BUSHMAN ss197914502 Jul 04, 2010 (132)
20 1000GENOMES ss218199153 Jul 14, 2010 (132)
21 1000GENOMES ss230401400 Jul 14, 2010 (132)
22 1000GENOMES ss238120591 Jul 15, 2010 (132)
23 BL ss252875944 May 09, 2011 (134)
24 GMI ss275689048 May 04, 2012 (137)
25 GMI ss283990150 Apr 25, 2013 (138)
26 PJP ss290497104 May 09, 2011 (134)
27 TISHKOFF ss553728175 Apr 25, 2013 (138)
28 SSMP ss647531389 Apr 25, 2013 (138)
29 EVA-GONL ss974788868 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1067622822 Aug 21, 2014 (142)
31 1000GENOMES ss1289423908 Aug 21, 2014 (142)
32 DDI ss1425690816 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1573857570 Apr 01, 2015 (144)
34 EVA_DECODE ss1584148349 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1599413495 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1642407528 Apr 01, 2015 (144)
37 HAMMER_LAB ss1793760475 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1917983975 Feb 12, 2016 (147)
39 GENOMED ss1966670141 Jul 19, 2016 (147)
40 JJLAB ss2019508131 Sep 14, 2016 (149)
41 USC_VALOUEV ss2147498219 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2159517631 Dec 20, 2016 (150)
43 TOPMED ss2321673294 Dec 20, 2016 (150)
44 SYSTEMSBIOZJU ss2624270031 Nov 08, 2017 (151)
45 GRF ss2697391860 Nov 08, 2017 (151)
46 GNOMAD ss2750897980 Nov 08, 2017 (151)
47 SWEGEN ss2986190401 Nov 08, 2017 (151)
48 BIOINF_KMB_FNS_UNIBA ss3023517832 Nov 08, 2017 (151)
49 TOPMED ss3066964607 Nov 08, 2017 (151)
50 CSHL ss3343285364 Nov 08, 2017 (151)
51 URBANLAB ss3646585452 Oct 11, 2018 (152)
52 EGCUT_WGS ss3654291463 Jul 12, 2019 (153)
53 EVA_DECODE ss3686033454 Jul 12, 2019 (153)
54 ACPOP ss3726733819 Jul 12, 2019 (153)
55 EVA ss3745746046 Jul 12, 2019 (153)
56 PACBIO ss3783307352 Jul 12, 2019 (153)
57 PACBIO ss3788984377 Jul 12, 2019 (153)
58 PACBIO ss3793857002 Jul 12, 2019 (153)
59 KHV_HUMAN_GENOMES ss3798768241 Jul 12, 2019 (153)
60 EVA ss3825990591 Apr 25, 2020 (154)
61 EVA ss3836382587 Apr 25, 2020 (154)
62 EVA ss3841786721 Apr 25, 2020 (154)
63 SGDP_PRJ ss3848053281 Apr 25, 2020 (154)
64 KRGDB ss3892913146 Apr 25, 2020 (154)
65 KOGIC ss3943676578 Apr 25, 2020 (154)
66 TOPMED ss4437093983 Apr 25, 2021 (155)
67 TOMMO_GENOMICS ss5142169762 Apr 25, 2021 (155)
68 1000Genomes NC_000001.10 - 3010317 Oct 11, 2018 (152)
69 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3010317 Oct 11, 2018 (152)
70 Genetic variation in the Estonian population NC_000001.10 - 3010317 Oct 11, 2018 (152)
71 The Danish reference pan genome NC_000001.10 - 3010317 Apr 25, 2020 (154)
72 gnomAD - Genomes NC_000001.11 - 3093753 Apr 25, 2021 (155)
73 Genome of the Netherlands Release 5 NC_000001.10 - 3010317 Apr 25, 2020 (154)
74 KOREAN population from KRGDB NC_000001.10 - 3010317 Apr 25, 2020 (154)
75 Korean Genome Project NC_000001.11 - 3093753 Apr 25, 2020 (154)
76 Northern Sweden NC_000001.10 - 3010317 Jul 12, 2019 (153)
77 Qatari NC_000001.10 - 3010317 Apr 25, 2020 (154)
78 SGDP_PRJ NC_000001.10 - 3010317 Apr 25, 2020 (154)
79 Siberian NC_000001.10 - 3010317 Apr 25, 2020 (154)
80 8.3KJPN NC_000001.10 - 3010317 Apr 25, 2021 (155)
81 TopMed NC_000001.11 - 3093753 Apr 25, 2021 (155)
82 UK 10K study - Twins NC_000001.10 - 3010317 Oct 11, 2018 (152)
83 ALFA NC_000001.11 - 3093753 Apr 25, 2021 (155)
Help

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)
rs58945970 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
9606057711 NC_000001.11:3093752:A:C NC_000001.11:3093752:A:C
ss78321732, ss82796670, ss83467748 NC_000001.8:3033473:A:T NC_000001.11:3093752:A:T (self)
ss107944806, ss109958776, ss118447888, ss162998158, ss163728895, ss197914502, ss252875944, ss275689048, ss283990150, ss290497104, ss1584148349 NC_000001.9:3000176:A:T NC_000001.11:3093752:A:T (self)
91079, 38629, 29711, 1364804, 16282, 90540, 18684, 25905, 70261, 14573, 139069, 38629, ss218199153, ss230401400, ss238120591, ss553728175, ss647531389, ss974788868, ss1067622822, ss1289423908, ss1425690816, ss1573857570, ss1599413495, ss1642407528, ss1793760475, ss1917983975, ss1966670141, ss2019508131, ss2147498219, ss2321673294, ss2624270031, ss2697391860, ss2750897980, ss2986190401, ss3343285364, ss3654291463, ss3726733819, ss3745746046, ss3783307352, ss3788984377, ss3793857002, ss3825990591, ss3836382587, ss3848053281, ss3892913146, ss5142169762 NC_000001.10:3010316:A:T NC_000001.11:3093752:A:T (self)
683085, 54579, 432526, 700318, 9606057711, ss2159517631, ss3023517832, ss3066964607, ss3646585452, ss3686033454, ss3798768241, ss3841786721, ss3943676578, ss4437093983 NC_000001.11:3093752:A:T NC_000001.11:3093752:A:T (self)
ss11346288, ss17353135, ss20452604 NT_004321.15:317091:A:T NC_000001.11:3093752:A:T (self)
ss133530, ss4214182, ss6396355, ss44112850, ss99180725, ss105114176, ss138984798 NT_004350.19:2488948:A:T NC_000001.11:3093752:A:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs760565

Help

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.

Software version is: 2.0.1.post596+ae089ad