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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.

rs4648358

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3077176 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.124043 (32833/264690, TOPMED)
T=0.143111 (20067/140220, GnomAD)
T=0.08925 (7023/78692, PAGE_STUDY) (+ 15 more)
T=0.17329 (3305/19072, ALFA)
T=0.07786 (1305/16760, 8.3KJPN)
T=0.1034 (518/5008, 1000G)
T=0.2679 (1200/4480, Estonian)
T=0.1892 (729/3854, ALSPAC)
T=0.1785 (662/3708, TWINSUK)
T=0.0643 (188/2922, KOREAN)
T=0.201 (201/998, GoNL)
T=0.175 (105/600, NorthernSweden)
T=0.236 (51/216, Qatari)
T=0.131 (28/214, Vietnamese)
G=0.411 (46/112, SGDP_PRJ)
T=0.12 (5/40, GENOME_DK)
G=0.50 (8/16, Siberian)
T=0.50 (8/16, 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.3077176G>T
GRCh37.p13 chr 1 NC_000001.10:g.2993740G>T
PRDM16 RefSeqGene NG_029576.2:g.12999G>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+7880G>T N/A Intron Variant
PRDM16 transcript variant 2 NM_199454.3:c.37+7880G>T 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 19072 G=0.82671 T=0.17329
European Sub 14364 G=0.79539 T=0.20461
African Sub 2954 G=0.9519 T=0.0481
African Others Sub 114 G=0.965 T=0.035
African American Sub 2840 G=0.9514 T=0.0486
Asian Sub 146 G=0.911 T=0.089
East Asian Sub 120 G=0.933 T=0.067
Other Asian Sub 26 G=0.81 T=0.19
Latin American 1 Sub 146 G=0.849 T=0.151
Latin American 2 Sub 610 G=0.884 T=0.116
South Asian Sub 104 G=0.837 T=0.163
Other Sub 748 G=0.865 T=0.135


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=0.875957 T=0.124043
gnomAD - Genomes Global Study-wide 140220 G=0.856889 T=0.143111
gnomAD - Genomes European Sub 75910 G=0.79423 T=0.20577
gnomAD - Genomes African Sub 42038 G=0.95204 T=0.04796
gnomAD - Genomes American Sub 13662 G=0.88867 T=0.11133
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.8905 T=0.1095
gnomAD - Genomes East Asian Sub 3132 G=0.9122 T=0.0878
gnomAD - Genomes Other Sub 2154 G=0.8742 T=0.1258
The PAGE Study Global Study-wide 78692 G=0.91075 T=0.08925
The PAGE Study AfricanAmerican Sub 32510 G=0.94377 T=0.05623
The PAGE Study Mexican Sub 10810 G=0.89750 T=0.10250
The PAGE Study Asian Sub 8316 G=0.9203 T=0.0797
The PAGE Study PuertoRican Sub 7918 G=0.8841 T=0.1159
The PAGE Study NativeHawaiian Sub 4534 G=0.8366 T=0.1634
The PAGE Study Cuban Sub 4228 G=0.8685 T=0.1315
The PAGE Study Dominican Sub 3828 G=0.8971 T=0.1029
The PAGE Study CentralAmerican Sub 2450 G=0.8804 T=0.1196
The PAGE Study SouthAmerican Sub 1982 G=0.8991 T=0.1009
The PAGE Study NativeAmerican Sub 1260 G=0.8460 T=0.1540
The PAGE Study SouthAsian Sub 856 G=0.850 T=0.150
8.3KJPN JAPANESE Study-wide 16760 G=0.92214 T=0.07786
1000Genomes Global Study-wide 5008 G=0.8966 T=0.1034
1000Genomes African Sub 1322 G=0.9849 T=0.0151
1000Genomes East Asian Sub 1008 G=0.9226 T=0.0774
1000Genomes Europe Sub 1006 G=0.8082 T=0.1918
1000Genomes South Asian Sub 978 G=0.834 T=0.166
1000Genomes American Sub 694 G=0.906 T=0.094
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7321 T=0.2679
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8108 T=0.1892
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8215 T=0.1785
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9357 T=0.0643
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.799 T=0.201
Northern Sweden ACPOP Study-wide 600 G=0.825 T=0.175
Qatari Global Study-wide 216 G=0.764 T=0.236
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.869 T=0.131
SGDP_PRJ Global Study-wide 112 G=0.411 T=0.589
The Danish reference pan genome Danish Study-wide 40 G=0.88 T=0.12
Siberian Global Study-wide 16 G=0.50 T=0.50
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= T
GRCh38.p13 chr 1 NC_000001.11:g.3077176= NC_000001.11:g.3077176G>T
GRCh37.p13 chr 1 NC_000001.10:g.2993740= NC_000001.10:g.2993740G>T
PRDM16 RefSeqGene NG_029576.2:g.12999= NG_029576.2:g.12999G>T
PRDM16 transcript variant 1 NM_022114.3:c.37+7880= NM_022114.3:c.37+7880G>T
PRDM16 transcript variant 1 NM_022114.4:c.37+7880= NM_022114.4:c.37+7880G>T
PRDM16 transcript variant 2 NM_199454.2:c.37+7880= NM_199454.2:c.37+7880G>T
PRDM16 transcript variant 2 NM_199454.3:c.37+7880= NM_199454.3:c.37+7880G>T
PRDM16 transcript variant X1 XM_005244772.1:c.37+7880= XM_005244772.1:c.37+7880G>T
PRDM16 transcript variant X2 XM_005244773.1:c.37+7880= XM_005244773.1:c.37+7880G>T
PRDM16 transcript variant X3 XM_005244774.1:c.37+7880= XM_005244774.1:c.37+7880G>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#.

45 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6396351 Feb 20, 2003 (111)
2 HGSV ss77817334 Dec 07, 2007 (129)
3 BUSHMAN ss197914193 Jul 04, 2010 (132)
4 BCM-HGSC-SUB ss205390358 Jul 04, 2010 (132)
5 1000GENOMES ss218199069 Jul 14, 2010 (132)
6 1000GENOMES ss230401330 Jul 14, 2010 (132)
7 1000GENOMES ss238120535 Jul 15, 2010 (132)
8 GMI ss275688990 May 04, 2012 (137)
9 GMI ss283990128 Apr 25, 2013 (138)
10 TISHKOFF ss553728052 Apr 25, 2013 (138)
11 SSMP ss647531280 Apr 25, 2013 (138)
12 EVA-GONL ss974788697 Aug 21, 2014 (142)
13 JMKIDD_LAB ss1067622730 Aug 21, 2014 (142)
14 1000GENOMES ss1289423240 Aug 21, 2014 (142)
15 EVA_GENOME_DK ss1573857499 Apr 01, 2015 (144)
16 EVA_DECODE ss1584148171 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1599413191 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1642407224 Apr 01, 2015 (144)
19 HAMMER_LAB ss1793760197 Sep 08, 2015 (146)
20 WEILL_CORNELL_DGM ss1917983807 Feb 12, 2016 (147)
21 ILLUMINA ss1958233595 Feb 12, 2016 (147)
22 JJLAB ss2019508041 Sep 14, 2016 (149)
23 USC_VALOUEV ss2147498123 Dec 20, 2016 (150)
24 HUMAN_LONGEVITY ss2159516241 Dec 20, 2016 (150)
25 TOPMED ss2321671863 Dec 20, 2016 (150)
26 GRF ss2697391767 Nov 08, 2017 (151)
27 SWEGEN ss2986190165 Nov 08, 2017 (151)
28 ILLUMINA ss3021046526 Nov 08, 2017 (151)
29 BIOINF_KMB_FNS_UNIBA ss3023517765 Nov 08, 2017 (151)
30 TOPMED ss3066960826 Nov 08, 2017 (151)
31 CSHL ss3343285287 Nov 08, 2017 (151)
32 ILLUMINA ss3651369126 Oct 11, 2018 (152)
33 EGCUT_WGS ss3654291172 Jul 12, 2019 (153)
34 EVA_DECODE ss3686033164 Jul 12, 2019 (153)
35 ILLUMINA ss3724990141 Jul 12, 2019 (153)
36 ACPOP ss3726733668 Jul 12, 2019 (153)
37 EVA ss3745745806 Jul 12, 2019 (153)
38 PAGE_CC ss3770780127 Jul 12, 2019 (153)
39 KHV_HUMAN_GENOMES ss3798768044 Jul 12, 2019 (153)
40 EVA ss3825990491 Apr 25, 2020 (154)
41 SGDP_PRJ ss3848052965 Apr 25, 2020 (154)
42 KRGDB ss3892912779 Apr 25, 2020 (154)
43 GNOMAD ss3987269478 Apr 25, 2021 (155)
44 TOPMED ss4437088863 Apr 25, 2021 (155)
45 TOMMO_GENOMICS ss5142169050 Apr 25, 2021 (155)
46 1000Genomes NC_000001.10 - 2993740 Oct 11, 2018 (152)
47 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 2993740 Oct 11, 2018 (152)
48 Genetic variation in the Estonian population NC_000001.10 - 2993740 Oct 11, 2018 (152)
49 The Danish reference pan genome NC_000001.10 - 2993740 Apr 25, 2020 (154)
50 gnomAD - Genomes NC_000001.11 - 3077176 Apr 25, 2021 (155)
51 Genome of the Netherlands Release 5 NC_000001.10 - 2993740 Apr 25, 2020 (154)
52 KOREAN population from KRGDB NC_000001.10 - 2993740 Apr 25, 2020 (154)
53 Northern Sweden NC_000001.10 - 2993740 Jul 12, 2019 (153)
54 The PAGE Study NC_000001.11 - 3077176 Jul 12, 2019 (153)
55 Qatari NC_000001.10 - 2993740 Apr 25, 2020 (154)
56 SGDP_PRJ NC_000001.10 - 2993740 Apr 25, 2020 (154)
57 Siberian NC_000001.10 - 2993740 Apr 25, 2020 (154)
58 8.3KJPN NC_000001.10 - 2993740 Apr 25, 2021 (155)
59 TopMed NC_000001.11 - 3077176 Apr 25, 2021 (155)
60 UK 10K study - Twins NC_000001.10 - 2993740 Oct 11, 2018 (152)
61 A Vietnamese Genetic Variation Database NC_000001.10 - 2993740 Jul 12, 2019 (153)
62 ALFA NC_000001.11 - 3077176 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
ss77817334 NC_000001.8:3016896:G:T NC_000001.11:3077175:G:T (self)
ss197914193, ss205390358, ss275688990, ss283990128, ss1584148171 NC_000001.9:2983599:G:T NC_000001.11:3077175:G:T (self)
90393, 38303, 29420, 1364733, 16124, 90173, 18533, 25737, 69945, 14477, 138357, 38303, 7868, ss218199069, ss230401330, ss238120535, ss553728052, ss647531280, ss974788697, ss1067622730, ss1289423240, ss1573857499, ss1599413191, ss1642407224, ss1793760197, ss1917983807, ss1958233595, ss2019508041, ss2147498123, ss2321671863, ss2697391767, ss2986190165, ss3021046526, ss3343285287, ss3651369126, ss3654291172, ss3726733668, ss3745745806, ss3825990491, ss3848052965, ss3892912779, ss5142169050 NC_000001.10:2993739:G:T NC_000001.11:3077175:G:T (self)
678926, 1596, 429191, 695198, 9050801067, ss2159516241, ss3023517765, ss3066960826, ss3686033164, ss3724990141, ss3770780127, ss3798768044, ss3987269478, ss4437088863 NC_000001.11:3077175:G:T NC_000001.11:3077175:G:T (self)
ss6396351 NT_004350.19:2472371:G:T NC_000001.11:3077175: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 rs4648358

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