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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.

rs4648359

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3077772 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.498315 (131899/264690, TOPMED)
C=0.487833 (68284/139974, GnomAD)
G=0.46655 (36642/78538, PAGE_STUDY) (+ 14 more)
G=0.49942 (9434/18890, ALFA)
G=0.10048 (1684/16760, 8.3KJPN)
G=0.4165 (2086/5008, 1000G)
G=0.4935 (2211/4480, Estonian)
G=0.4940 (1904/3854, ALSPAC)
G=0.4835 (1793/3708, TWINSUK)
G=0.1034 (303/2930, KOREAN)
G=0.1272 (233/1832, Korea1K)
C=0.481 (480/998, GoNL)
G=0.412 (247/600, NorthernSweden)
G=0.222 (103/464, SGDP_PRJ)
C=0.412 (89/216, Qatari)
G=0.28 (14/50, Siberian)
G=0.47 (19/40, 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.3077772G>A
GRCh38.p13 chr 1 NC_000001.11:g.3077772G>C
GRCh38.p13 chr 1 NC_000001.11:g.3077772G>T
GRCh37.p13 chr 1 NC_000001.10:g.2994336G>A
GRCh37.p13 chr 1 NC_000001.10:g.2994336G>C
GRCh37.p13 chr 1 NC_000001.10:g.2994336G>T
PRDM16 RefSeqGene NG_029576.2:g.13595G>A
PRDM16 RefSeqGene NG_029576.2:g.13595G>C
PRDM16 RefSeqGene NG_029576.2:g.13595G>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+8476G>A N/A Intron Variant
PRDM16 transcript variant 2 NM_199454.3:c.37+8476G>A 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 18890 G=0.49942 C=0.50058
European Sub 14286 G=0.48810 C=0.51190
African Sub 2946 G=0.6015 C=0.3985
African Others Sub 114 G=0.623 C=0.377
African American Sub 2832 G=0.6006 C=0.3994
Asian Sub 112 G=0.170 C=0.830
East Asian Sub 86 G=0.14 C=0.86
Other Asian Sub 26 G=0.27 C=0.73
Latin American 1 Sub 146 G=0.473 C=0.527
Latin American 2 Sub 610 G=0.382 C=0.618
South Asian Sub 98 G=0.41 C=0.59
Other Sub 692 G=0.474 C=0.526


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 G=0.498315 C=0.501685
gnomAD - Genomes Global Study-wide 139974 G=0.512167 C=0.487833
gnomAD - Genomes European Sub 75826 G=0.49542 C=0.50458
gnomAD - Genomes African Sub 41906 G=0.60545 C=0.39455
gnomAD - Genomes American Sub 13646 G=0.43243 C=0.56757
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.4114 C=0.5886
gnomAD - Genomes East Asian Sub 3124 G=0.1316 C=0.8684
gnomAD - Genomes Other Sub 2154 G=0.4991 C=0.5009
The PAGE Study Global Study-wide 78538 G=0.46655 C=0.53345
The PAGE Study AfricanAmerican Sub 32408 G=0.60331 C=0.39669
The PAGE Study Mexican Sub 10798 G=0.37461 C=0.62539
The PAGE Study Asian Sub 8314 G=0.1146 C=0.8854
The PAGE Study PuertoRican Sub 7910 G=0.4862 C=0.5138
The PAGE Study NativeHawaiian Sub 4528 G=0.2772 C=0.7228
The PAGE Study Cuban Sub 4222 G=0.4998 C=0.5002
The PAGE Study Dominican Sub 3824 G=0.5434 C=0.4566
The PAGE Study CentralAmerican Sub 2448 G=0.4477 C=0.5523
The PAGE Study SouthAmerican Sub 1976 G=0.3750 C=0.6250
The PAGE Study NativeAmerican Sub 1258 G=0.4921 C=0.5079
The PAGE Study SouthAsian Sub 852 G=0.407 C=0.593
8.3KJPN JAPANESE Study-wide 16760 G=0.10048 C=0.89952
1000Genomes Global Study-wide 5008 G=0.4165 C=0.5835
1000Genomes African Sub 1322 G=0.6241 C=0.3759
1000Genomes East Asian Sub 1008 G=0.1210 C=0.8790
1000Genomes Europe Sub 1006 G=0.4861 C=0.5139
1000Genomes South Asian Sub 978 G=0.359 C=0.641
1000Genomes American Sub 694 G=0.431 C=0.569
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.4935 C=0.5065
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.4940 C=0.5060
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.4835 C=0.5165
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.1034 A=0.0000, C=0.8966, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 G=0.1272 C=0.8728
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.519 C=0.481
Northern Sweden ACPOP Study-wide 600 G=0.412 C=0.588
SGDP_PRJ Global Study-wide 464 G=0.222 C=0.778
Qatari Global Study-wide 216 G=0.588 C=0.412
Siberian Global Study-wide 50 G=0.28 C=0.72
The Danish reference pan genome Danish Study-wide 40 G=0.47 C=0.53
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 G= A C T
GRCh38.p13 chr 1 NC_000001.11:g.3077772= NC_000001.11:g.3077772G>A NC_000001.11:g.3077772G>C NC_000001.11:g.3077772G>T
GRCh37.p13 chr 1 NC_000001.10:g.2994336= NC_000001.10:g.2994336G>A NC_000001.10:g.2994336G>C NC_000001.10:g.2994336G>T
PRDM16 RefSeqGene NG_029576.2:g.13595= NG_029576.2:g.13595G>A NG_029576.2:g.13595G>C NG_029576.2:g.13595G>T
PRDM16 transcript variant 1 NM_022114.3:c.37+8476= NM_022114.3:c.37+8476G>A NM_022114.3:c.37+8476G>C NM_022114.3:c.37+8476G>T
PRDM16 transcript variant 1 NM_022114.4:c.37+8476= NM_022114.4:c.37+8476G>A NM_022114.4:c.37+8476G>C NM_022114.4:c.37+8476G>T
PRDM16 transcript variant 2 NM_199454.2:c.37+8476= NM_199454.2:c.37+8476G>A NM_199454.2:c.37+8476G>C NM_199454.2:c.37+8476G>T
PRDM16 transcript variant 2 NM_199454.3:c.37+8476= NM_199454.3:c.37+8476G>A NM_199454.3:c.37+8476G>C NM_199454.3:c.37+8476G>T
PRDM16 transcript variant X1 XM_005244772.1:c.37+8476= XM_005244772.1:c.37+8476G>A XM_005244772.1:c.37+8476G>C XM_005244772.1:c.37+8476G>T
PRDM16 transcript variant X2 XM_005244773.1:c.37+8476= XM_005244773.1:c.37+8476G>A XM_005244773.1:c.37+8476G>C XM_005244773.1:c.37+8476G>T
PRDM16 transcript variant X3 XM_005244774.1:c.37+8476= XM_005244774.1:c.37+8476G>A XM_005244774.1:c.37+8476G>C XM_005244774.1:c.37+8476G>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#.

75 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6396352 Feb 20, 2003 (111)
2 SSAHASNP ss20433777 Apr 05, 2004 (121)
3 ABI ss43863410 Mar 13, 2006 (126)
4 HGSV ss78701452 Dec 07, 2007 (129)
5 BCMHGSC_JDW ss87170086 Mar 23, 2008 (129)
6 HUMANGENOME_JCVI ss97915098 Feb 05, 2009 (130)
7 BGI ss105114159 Dec 01, 2009 (131)
8 1000GENOMES ss107944610 Jan 22, 2009 (130)
9 ILLUMINA-UK ss118447768 Feb 14, 2009 (130)
10 ENSEMBL ss137760979 Dec 01, 2009 (131)
11 ENSEMBL ss143012068 Dec 01, 2009 (131)
12 GMI ss154550807 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss163728475 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss165999974 Jul 04, 2010 (132)
15 1000GENOMES ss218199071 Jul 14, 2010 (132)
16 1000GENOMES ss230401333 Jul 14, 2010 (132)
17 1000GENOMES ss238120538 Jul 15, 2010 (132)
18 GMI ss275688993 May 04, 2012 (137)
19 PJP ss290497057 May 09, 2011 (134)
20 ILLUMINA ss482310424 May 04, 2012 (137)
21 ILLUMINA ss483203487 May 04, 2012 (137)
22 ILLUMINA ss535423474 Sep 08, 2015 (146)
23 TISHKOFF ss553728060 Apr 25, 2013 (138)
24 SSMP ss647531284 Apr 25, 2013 (138)
25 ILLUMINA ss780189639 Sep 08, 2015 (146)
26 ILLUMINA ss782045051 Sep 08, 2015 (146)
27 ILLUMINA ss835673992 Sep 08, 2015 (146)
28 EVA-GONL ss974788701 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1067622733 Aug 21, 2014 (142)
30 1000GENOMES ss1289423263 Aug 21, 2014 (142)
31 DDI ss1425690763 Apr 01, 2015 (144)
32 EVA_GENOME_DK ss1573857502 Apr 01, 2015 (144)
33 EVA_DECODE ss1584148175 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1599413204 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1642407237 Apr 01, 2015 (144)
36 HAMMER_LAB ss1793760203 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1917983814 Feb 12, 2016 (147)
38 ILLUMINA ss1958233596 Feb 12, 2016 (147)
39 JJLAB ss2019508045 Sep 14, 2016 (149)
40 USC_VALOUEV ss2147498127 Dec 20, 2016 (150)
41 HUMAN_LONGEVITY ss2159516286 Dec 20, 2016 (150)
42 TOPMED ss2321671906 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2624269988 Nov 08, 2017 (151)
44 ILLUMINA ss2632467550 Nov 08, 2017 (151)
45 GRF ss2697391771 Nov 08, 2017 (151)
46 GNOMAD ss2750896307 Nov 08, 2017 (151)
47 AFFY ss2985495619 Nov 08, 2017 (151)
48 SWEGEN ss2986190171 Nov 08, 2017 (151)
49 ILLUMINA ss3021046528 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3023517768 Nov 08, 2017 (151)
51 TOPMED ss3066960943 Nov 08, 2017 (151)
52 CSHL ss3343285291 Nov 08, 2017 (151)
53 ILLUMINA ss3626010214 Oct 11, 2018 (152)
54 ILLUMINA ss3630507108 Oct 11, 2018 (152)
55 ILLUMINA ss3641567253 Oct 11, 2018 (152)
56 URBANLAB ss3646585398 Oct 11, 2018 (152)
57 ILLUMINA ss3651369128 Oct 11, 2018 (152)
58 EGCUT_WGS ss3654291179 Jul 12, 2019 (153)
59 EVA_DECODE ss3686033171 Jul 12, 2019 (153)
60 ILLUMINA ss3724990143 Jul 12, 2019 (153)
61 ACPOP ss3726733672 Jul 12, 2019 (153)
62 EVA ss3745745814 Jul 12, 2019 (153)
63 PAGE_CC ss3770780128 Jul 12, 2019 (153)
64 PACBIO ss3783307295 Jul 12, 2019 (153)
65 PACBIO ss3788984323 Jul 12, 2019 (153)
66 PACBIO ss3793856948 Jul 12, 2019 (153)
67 KHV_HUMAN_GENOMES ss3798768048 Jul 12, 2019 (153)
68 EVA ss3825990495 Apr 25, 2020 (154)
69 EVA ss3836382523 Apr 25, 2020 (154)
70 EVA ss3841786657 Apr 25, 2020 (154)
71 SGDP_PRJ ss3848052976 Apr 25, 2020 (154)
72 KRGDB ss3892912792 Apr 25, 2020 (154)
73 KOGIC ss3943676194 Apr 25, 2020 (154)
74 TOPMED ss4437089038 Apr 25, 2021 (155)
75 TOMMO_GENOMICS ss5142169072 Apr 25, 2021 (155)
76 1000Genomes NC_000001.10 - 2994336 Oct 11, 2018 (152)
77 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 2994336 Oct 11, 2018 (152)
78 Genetic variation in the Estonian population NC_000001.10 - 2994336 Oct 11, 2018 (152)
79 The Danish reference pan genome NC_000001.10 - 2994336 Apr 25, 2020 (154)
80 gnomAD - Genomes NC_000001.11 - 3077772 Apr 25, 2021 (155)
81 Genome of the Netherlands Release 5 NC_000001.10 - 2994336 Apr 25, 2020 (154)
82 KOREAN population from KRGDB NC_000001.10 - 2994336 Apr 25, 2020 (154)
83 Korean Genome Project NC_000001.11 - 3077772 Apr 25, 2020 (154)
84 Northern Sweden NC_000001.10 - 2994336 Jul 12, 2019 (153)
85 The PAGE Study NC_000001.11 - 3077772 Jul 12, 2019 (153)
86 Qatari NC_000001.10 - 2994336 Apr 25, 2020 (154)
87 SGDP_PRJ NC_000001.10 - 2994336 Apr 25, 2020 (154)
88 Siberian NC_000001.10 - 2994336 Apr 25, 2020 (154)
89 8.3KJPN NC_000001.10 - 2994336 Apr 25, 2021 (155)
90 TopMed NC_000001.11 - 3077772 Apr 25, 2021 (155)
91 UK 10K study - Twins NC_000001.10 - 2994336 Oct 11, 2018 (152)
92 ALFA NC_000001.11 - 3077772 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
90186, ss3892912792 NC_000001.10:2994335:G:A NC_000001.11:3077771:G:A (self)
ss78701452 NC_000001.8:3017492:G:C NC_000001.11:3077771:G:C (self)
ss87170086, ss107944610, ss118447768, ss163728475, ss165999974, ss275688993, ss290497057, ss482310424, ss1584148175 NC_000001.9:2984195:G:C NC_000001.11:3077771:G:C (self)
90416, 38316, 29427, 1364736, 16128, 90186, 18537, 25744, 69956, 14481, 138379, 38316, ss218199071, ss230401333, ss238120538, ss483203487, ss535423474, ss553728060, ss647531284, ss780189639, ss782045051, ss835673992, ss974788701, ss1067622733, ss1289423263, ss1425690763, ss1573857502, ss1599413204, ss1642407237, ss1793760203, ss1917983814, ss1958233596, ss2019508045, ss2147498127, ss2321671906, ss2624269988, ss2632467550, ss2697391771, ss2750896307, ss2985495619, ss2986190171, ss3021046528, ss3343285291, ss3626010214, ss3630507108, ss3641567253, ss3651369128, ss3654291179, ss3726733672, ss3745745814, ss3783307295, ss3788984323, ss3793856948, ss3825990495, ss3836382523, ss3848052976, ss3892912792, ss5142169072 NC_000001.10:2994335:G:C NC_000001.11:3077771:G:C (self)
679060, 54195, 1597, 429300, 695373, 6283192159, ss2159516286, ss3023517768, ss3066960943, ss3646585398, ss3686033171, ss3724990143, ss3770780128, ss3798768048, ss3841786657, ss3943676194, ss4437089038 NC_000001.11:3077771:G:C NC_000001.11:3077771:G:C (self)
ss20433777 NT_004321.15:301110:G:C NC_000001.11:3077771:G:C (self)
ss6396352, ss43863410, ss97915098, ss105114159, ss137760979, ss143012068, ss154550807 NT_004350.19:2472967:G:C NC_000001.11:3077771:G:C (self)
90186, ss3892912792 NC_000001.10:2994335:G:T NC_000001.11:3077771:G: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 rs4648359

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