Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs4648362

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3095810 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.363886 (96317/264690, TOPMED)
C=0.45871 (7688/16760, 8.3KJPN)
G=0.14458 (1785/12346, ALFA) (+ 13 more)
G=0.4357 (2182/5008, 1000G)
G=0.2424 (1086/4480, Estonian)
G=0.2514 (969/3854, ALSPAC)
G=0.2638 (978/3708, TWINSUK)
G=0.4730 (1386/2930, KOREAN)
G=0.4689 (859/1832, Korea1K)
G=0.269 (268/998, GoNL)
G=0.270 (162/600, NorthernSweden)
C=0.339 (118/348, SGDP_PRJ)
G=0.491 (106/216, Qatari)
C=0.425 (91/214, Vietnamese)
G=0.10 (4/40, GENOME_DK)
C=0.47 (15/32, Siberian)
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.3095810C>A
GRCh38.p13 chr 1 NC_000001.11:g.3095810C>G
GRCh38.p13 chr 1 NC_000001.11:g.3095810C>T
GRCh37.p13 chr 1 NC_000001.10:g.3012374C>A
GRCh37.p13 chr 1 NC_000001.10:g.3012374C>G
GRCh37.p13 chr 1 NC_000001.10:g.3012374C>T
PRDM16 RefSeqGene NG_029576.2:g.31633C>A
PRDM16 RefSeqGene NG_029576.2:g.31633C>G
PRDM16 RefSeqGene NG_029576.2:g.31633C>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+26514C>A N/A Intron Variant
PRDM16 transcript variant 2 NM_199454.3:c.37+26514C>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 12346 C=0.85542 A=0.00000, G=0.14458, T=0.00000
European Sub 10840 C=0.84843 A=0.00000, G=0.15157, T=0.00000
African Sub 706 C=0.902 A=0.000, G=0.098, T=0.000
African Others Sub 30 C=0.87 A=0.00, G=0.13, T=0.00
African American Sub 676 C=0.904 A=0.000, G=0.096, T=0.000
Asian Sub 18 C=0.89 A=0.00, G=0.11, T=0.00
East Asian Sub 12 C=0.92 A=0.00, G=0.08, T=0.00
Other Asian Sub 6 C=0.8 A=0.0, G=0.2, T=0.0
Latin American 1 Sub 40 C=1.00 A=0.00, G=0.00, T=0.00
Latin American 2 Sub 290 C=1.000 A=0.000, G=0.000, T=0.000
South Asian Sub 34 C=0.91 A=0.00, G=0.09, T=0.00
Other Sub 418 C=0.837 A=0.000, G=0.163, T=0.000


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 C=0.636114 G=0.363886
8.3KJPN JAPANESE Study-wide 16760 C=0.45871 G=0.54129
1000Genomes Global Study-wide 5008 C=0.5643 G=0.4357
1000Genomes African Sub 1322 C=0.4153 G=0.5847
1000Genomes East Asian Sub 1008 C=0.4950 G=0.5050
1000Genomes Europe Sub 1006 C=0.7416 G=0.2584
1000Genomes South Asian Sub 978 C=0.552 G=0.448
1000Genomes American Sub 694 C=0.709 G=0.291
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.7576 G=0.2424
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7486 G=0.2514
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7362 G=0.2638
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.5270 G=0.4730
Korean Genome Project KOREAN Study-wide 1832 C=0.5311 G=0.4689
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.731 G=0.269
Northern Sweden ACPOP Study-wide 600 C=0.730 G=0.270
SGDP_PRJ Global Study-wide 348 C=0.339 G=0.661
Qatari Global Study-wide 216 C=0.509 G=0.491
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.425 G=0.575
The Danish reference pan genome Danish Study-wide 40 C=0.90 G=0.10
Siberian Global Study-wide 32 C=0.47 G=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 C= A G T
GRCh38.p13 chr 1 NC_000001.11:g.3095810= NC_000001.11:g.3095810C>A NC_000001.11:g.3095810C>G NC_000001.11:g.3095810C>T
GRCh37.p13 chr 1 NC_000001.10:g.3012374= NC_000001.10:g.3012374C>A NC_000001.10:g.3012374C>G NC_000001.10:g.3012374C>T
PRDM16 RefSeqGene NG_029576.2:g.31633= NG_029576.2:g.31633C>A NG_029576.2:g.31633C>G NG_029576.2:g.31633C>T
PRDM16 transcript variant 1 NM_022114.3:c.37+26514= NM_022114.3:c.37+26514C>A NM_022114.3:c.37+26514C>G NM_022114.3:c.37+26514C>T
PRDM16 transcript variant 1 NM_022114.4:c.37+26514= NM_022114.4:c.37+26514C>A NM_022114.4:c.37+26514C>G NM_022114.4:c.37+26514C>T
PRDM16 transcript variant 2 NM_199454.2:c.37+26514= NM_199454.2:c.37+26514C>A NM_199454.2:c.37+26514C>G NM_199454.2:c.37+26514C>T
PRDM16 transcript variant 2 NM_199454.3:c.37+26514= NM_199454.3:c.37+26514C>A NM_199454.3:c.37+26514C>G NM_199454.3:c.37+26514C>T
PRDM16 transcript variant X1 XM_005244772.1:c.37+26514= XM_005244772.1:c.37+26514C>A XM_005244772.1:c.37+26514C>G XM_005244772.1:c.37+26514C>T
PRDM16 transcript variant X2 XM_005244773.1:c.37+26514= XM_005244773.1:c.37+26514C>A XM_005244773.1:c.37+26514C>G XM_005244773.1:c.37+26514C>T
PRDM16 transcript variant X3 XM_005244774.1:c.37+26514= XM_005244774.1:c.37+26514C>A XM_005244774.1:c.37+26514C>G XM_005244774.1:c.37+26514C>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#.

56 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6396357 Feb 20, 2003 (111)
2 CSHL-HAPMAP ss17354362 Feb 27, 2004 (120)
3 ABI ss43986348 Mar 13, 2006 (126)
4 BGI ss105114186 Dec 01, 2009 (131)
5 1000GENOMES ss109958847 Jan 24, 2009 (130)
6 ILLUMINA-UK ss118447922 Feb 14, 2009 (130)
7 ENSEMBL ss161244648 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss162998208 Jul 04, 2010 (132)
9 BUSHMAN ss197914576 Jul 04, 2010 (132)
10 1000GENOMES ss218199174 Jul 14, 2010 (132)
11 1000GENOMES ss230401412 Jul 14, 2010 (132)
12 1000GENOMES ss238120602 Jul 15, 2010 (132)
13 BL ss252875980 May 09, 2011 (134)
14 GMI ss275689060 May 04, 2012 (137)
15 GMI ss283990155 Apr 25, 2013 (138)
16 TISHKOFF ss553728200 Apr 25, 2013 (138)
17 SSMP ss647531407 Apr 25, 2013 (138)
18 EVA-GONL ss974788895 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1067622838 Aug 21, 2014 (142)
20 1000GENOMES ss1289424002 Aug 21, 2014 (142)
21 DDI ss1425690826 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1573857583 Apr 01, 2015 (144)
23 EVA_DECODE ss1584148376 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1599413551 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1642407584 Apr 01, 2015 (144)
26 HAMMER_LAB ss1793760557 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1917984004 Feb 12, 2016 (147)
28 GENOMED ss1966670149 Jul 19, 2016 (147)
29 JJLAB ss2019508148 Sep 14, 2016 (149)
30 USC_VALOUEV ss2147498233 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2159517822 Dec 20, 2016 (150)
32 TOPMED ss2321673480 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2624270042 Nov 08, 2017 (151)
34 GRF ss2697391874 Nov 08, 2017 (151)
35 GNOMAD ss2750898220 Nov 08, 2017 (151)
36 AFFY ss2985495693 Nov 08, 2017 (151)
37 SWEGEN ss2986190433 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3023517843 Nov 08, 2017 (151)
39 TOPMED ss3066965069 Nov 08, 2017 (151)
40 TOPMED ss3066965070 Nov 08, 2017 (151)
41 TOPMED ss3066965071 Nov 08, 2017 (151)
42 CSHL ss3343285376 Nov 08, 2017 (151)
43 EGCUT_WGS ss3654291501 Jul 12, 2019 (153)
44 EVA_DECODE ss3686033491 Jul 12, 2019 (153)
45 ACPOP ss3726733840 Jul 12, 2019 (153)
46 EVA ss3745746086 Jul 12, 2019 (153)
47 PACBIO ss3783307362 Jul 12, 2019 (153)
48 PACBIO ss3788984387 Jul 12, 2019 (153)
49 PACBIO ss3793857012 Jul 12, 2019 (153)
50 KHV_HUMAN_GENOMES ss3798768276 Jul 12, 2019 (153)
51 EVA ss3825990608 Apr 25, 2020 (154)
52 SGDP_PRJ ss3848053332 Apr 25, 2020 (154)
53 KRGDB ss3892913197 Apr 25, 2020 (154)
54 KOGIC ss3943676636 Apr 25, 2020 (154)
55 TOPMED ss4437094620 Apr 25, 2021 (155)
56 TOMMO_GENOMICS ss5142169847 Apr 25, 2021 (155)
57 1000Genomes NC_000001.10 - 3012374 Oct 11, 2018 (152)
58 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3012374 Oct 11, 2018 (152)
59 Genetic variation in the Estonian population NC_000001.10 - 3012374 Oct 11, 2018 (152)
60 The Danish reference pan genome NC_000001.10 - 3012374 Apr 25, 2020 (154)
61 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 683619 (NC_000001.11:3095809:C:A 2/139950)
Row 683620 (NC_000001.11:3095809:C:G 49210/139902)
Row 683621 (NC_000001.11:3095809:C:T 2/139950)

- Apr 25, 2021 (155)
62 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 683619 (NC_000001.11:3095809:C:A 2/139950)
Row 683620 (NC_000001.11:3095809:C:G 49210/139902)
Row 683621 (NC_000001.11:3095809:C:T 2/139950)

- Apr 25, 2021 (155)
63 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 683619 (NC_000001.11:3095809:C:A 2/139950)
Row 683620 (NC_000001.11:3095809:C:G 49210/139902)
Row 683621 (NC_000001.11:3095809:C:T 2/139950)

- Apr 25, 2021 (155)
64 Genome of the Netherlands Release 5 NC_000001.10 - 3012374 Apr 25, 2020 (154)
65 KOREAN population from KRGDB NC_000001.10 - 3012374 Apr 25, 2020 (154)
66 Korean Genome Project NC_000001.11 - 3095810 Apr 25, 2020 (154)
67 Northern Sweden NC_000001.10 - 3012374 Jul 12, 2019 (153)
68 Qatari NC_000001.10 - 3012374 Apr 25, 2020 (154)
69 SGDP_PRJ NC_000001.10 - 3012374 Apr 25, 2020 (154)
70 Siberian NC_000001.10 - 3012374 Apr 25, 2020 (154)
71 8.3KJPN NC_000001.10 - 3012374 Apr 25, 2021 (155)
72 TopMed NC_000001.11 - 3095810 Apr 25, 2021 (155)
73 UK 10K study - Twins NC_000001.10 - 3012374 Oct 11, 2018 (152)
74 A Vietnamese Genetic Variation Database NC_000001.10 - 3012374 Jul 12, 2019 (153)
75 ALFA NC_000001.11 - 3095810 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
ss2750898220 NC_000001.10:3012373:C:A NC_000001.11:3095809:C:A (self)
6192890607, ss3066965069 NC_000001.11:3095809:C:A NC_000001.11:3095809:C:A (self)
ss109958847, ss118447922, ss162998208, ss197914576, ss252875980, ss275689060, ss283990155, ss1584148376 NC_000001.9:3002233:C:G NC_000001.11:3095809:C:G (self)
91177, 38688, 29749, 1364817, 16309, 90591, 18705, 25934, 70312, 14587, 139154, 38688, 7981, ss218199174, ss230401412, ss238120602, ss553728200, ss647531407, ss974788895, ss1067622838, ss1289424002, ss1425690826, ss1573857583, ss1599413551, ss1642407584, ss1793760557, ss1917984004, ss1966670149, ss2019508148, ss2147498233, ss2321673480, ss2624270042, ss2697391874, ss2750898220, ss2985495693, ss2986190433, ss3343285376, ss3654291501, ss3726733840, ss3745746086, ss3783307362, ss3788984387, ss3793857012, ss3825990608, ss3848053332, ss3892913197, ss5142169847 NC_000001.10:3012373:C:G NC_000001.11:3095809:C:G (self)
54637, 432942, 700955, 6192890607, ss2159517822, ss3023517843, ss3066965070, ss3686033491, ss3798768276, ss3943676636, ss4437094620 NC_000001.11:3095809:C:G NC_000001.11:3095809:C:G (self)
ss17354362 NT_004321.15:319148:C:G NC_000001.11:3095809:C:G (self)
ss6396357, ss43986348, ss105114186, ss161244648 NT_004350.19:2491005:C:G NC_000001.11:3095809:C:G (self)
6192890607, ss3066965071 NC_000001.11:3095809:C:T NC_000001.11:3095809:C: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 rs4648362

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