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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.

rs7528821

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:3581819 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.213998 (56643/264690, TOPMED)
T=0.201651 (28219/139940, GnomAD)
T=0.25430 (7184/28250, 14KJPN) (+ 15 more)
T=0.18248 (3447/18890, ALFA)
T=0.25725 (4311/16758, 8.3KJPN)
T=0.2500 (1601/6404, 1000G_30x)
T=0.2462 (1233/5008, 1000G)
T=0.1560 (699/4480, Estonian)
T=0.1684 (649/3854, ALSPAC)
T=0.1524 (565/3708, TWINSUK)
T=0.2633 (771/2928, KOREAN)
T=0.2680 (491/1832, Korea1K)
T=0.162 (162/998, GoNL)
T=0.143 (86/600, NorthernSweden)
C=0.432 (95/220, SGDP_PRJ)
T=0.194 (42/216, Qatari)
T=0.07 (3/40, GENOME_DK)
C=0.45 (10/22, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MEGF6 : 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 C=0.81752 T=0.18248
European Sub 14286 C=0.84523 T=0.15477
African Sub 2946 C=0.7010 T=0.2990
African Others Sub 114 C=0.667 T=0.333
African American Sub 2832 C=0.7023 T=0.2977
Asian Sub 112 C=0.652 T=0.348
East Asian Sub 86 C=0.72 T=0.28
Other Asian Sub 26 C=0.42 T=0.58
Latin American 1 Sub 146 C=0.863 T=0.137
Latin American 2 Sub 610 C=0.802 T=0.198
South Asian Sub 98 C=0.80 T=0.20
Other Sub 692 C=0.776 T=0.224


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=0.786002 T=0.213998
gnomAD - Genomes Global Study-wide 139940 C=0.798349 T=0.201651
gnomAD - Genomes European Sub 75830 C=0.85214 T=0.14786
gnomAD - Genomes African Sub 41880 C=0.70907 T=0.29093
gnomAD - Genomes American Sub 13638 C=0.78054 T=0.21946
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.8718 T=0.1282
gnomAD - Genomes East Asian Sub 3124 C=0.6997 T=0.3003
gnomAD - Genomes Other Sub 2144 C=0.7826 T=0.2174
14KJPN JAPANESE Study-wide 28250 C=0.74570 T=0.25430
Allele Frequency Aggregator Total Global 18890 C=0.81752 T=0.18248
Allele Frequency Aggregator European Sub 14286 C=0.84523 T=0.15477
Allele Frequency Aggregator African Sub 2946 C=0.7010 T=0.2990
Allele Frequency Aggregator Other Sub 692 C=0.776 T=0.224
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.802 T=0.198
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.863 T=0.137
Allele Frequency Aggregator Asian Sub 112 C=0.652 T=0.348
Allele Frequency Aggregator South Asian Sub 98 C=0.80 T=0.20
8.3KJPN JAPANESE Study-wide 16758 C=0.74275 T=0.25725
1000Genomes_30x Global Study-wide 6404 C=0.7500 T=0.2500
1000Genomes_30x African Sub 1786 C=0.6831 T=0.3169
1000Genomes_30x Europe Sub 1266 C=0.8507 T=0.1493
1000Genomes_30x South Asian Sub 1202 C=0.7862 T=0.2138
1000Genomes_30x East Asian Sub 1170 C=0.6872 T=0.3128
1000Genomes_30x American Sub 980 C=0.772 T=0.228
1000Genomes Global Study-wide 5008 C=0.7538 T=0.2462
1000Genomes African Sub 1322 C=0.6884 T=0.3116
1000Genomes East Asian Sub 1008 C=0.6984 T=0.3016
1000Genomes Europe Sub 1006 C=0.8499 T=0.1501
1000Genomes South Asian Sub 978 C=0.789 T=0.211
1000Genomes American Sub 694 C=0.769 T=0.231
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8440 T=0.1560
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8316 T=0.1684
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8476 T=0.1524
KOREAN population from KRGDB KOREAN Study-wide 2928 C=0.7367 T=0.2633
Korean Genome Project KOREAN Study-wide 1832 C=0.7320 T=0.2680
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.838 T=0.162
Northern Sweden ACPOP Study-wide 600 C=0.857 T=0.143
SGDP_PRJ Global Study-wide 220 C=0.432 T=0.568
Qatari Global Study-wide 216 C=0.806 T=0.194
The Danish reference pan genome Danish Study-wide 40 C=0.93 T=0.07
Siberian Global Study-wide 22 C=0.45 T=0.55
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.p14 chr 1 NC_000001.11:g.3581819C>T
GRCh37.p13 chr 1 NC_000001.10:g.3498383C>T
Gene: MEGF6, multiple EGF like domains 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MEGF6 transcript variant 1 NM_001409.4:c.377-1890G>A N/A Intron Variant
MEGF6 transcript variant X1 XM_011540886.3:c.563-1890…

XM_011540886.3:c.563-1890G>A

N/A Intron Variant
MEGF6 transcript variant X15 XM_011540888.4:c.563-1890…

XM_011540888.4:c.563-1890G>A

N/A Intron Variant
MEGF6 transcript variant X2 XM_017000533.3:c.563-1890…

XM_017000533.3:c.563-1890G>A

N/A Intron Variant
MEGF6 transcript variant X3 XM_047448204.1:c.377-1890…

XM_047448204.1:c.377-1890G>A

N/A Intron Variant
MEGF6 transcript variant X4 XM_047448205.1:c.377-1890…

XM_047448205.1:c.377-1890G>A

N/A Intron Variant
MEGF6 transcript variant X5 XM_047448215.1:c.377-1890…

XM_047448215.1:c.377-1890G>A

N/A Intron Variant
MEGF6 transcript variant X6 XM_047448217.1:c.377-1890…

XM_047448217.1:c.377-1890G>A

N/A Intron Variant
MEGF6 transcript variant X7 XM_047448220.1:c.377-1890…

XM_047448220.1:c.377-1890G>A

N/A Intron Variant
MEGF6 transcript variant X8 XM_047448221.1:c.377-1890…

XM_047448221.1:c.377-1890G>A

N/A Intron Variant
MEGF6 transcript variant X9 XM_047448228.1:c.377-1890…

XM_047448228.1:c.377-1890G>A

N/A Intron Variant
MEGF6 transcript variant X10 XM_047448229.1:c.377-1890…

XM_047448229.1:c.377-1890G>A

N/A Intron Variant
MEGF6 transcript variant X11 XM_047448232.1:c.377-1890…

XM_047448232.1:c.377-1890G>A

N/A Intron Variant
MEGF6 transcript variant X10 XM_006710406.5:c. N/A Genic Upstream Transcript Variant
MEGF6 transcript variant X12 XM_011540887.3:c. N/A Genic Upstream Transcript Variant
MEGF6 transcript variant X13 XM_047448238.1:c. N/A Genic Upstream Transcript Variant
MEGF6 transcript variant X14 XM_047448239.1:c. N/A Genic Upstream Transcript Variant
MEGF6 transcript variant X16 XM_047448242.1:c. N/A Genic Upstream Transcript Variant
MEGF6 transcript variant X17 XM_047448245.1:c. N/A Genic Upstream Transcript Variant
MEGF6 transcript variant X18 XM_047448247.1:c. N/A Genic Upstream Transcript Variant
MEGF6 transcript variant X19 XM_047448251.1:c. N/A Genic Upstream Transcript Variant
MEGF6 transcript variant X20 XM_047448255.1:c. N/A Genic Upstream Transcript Variant
MEGF6 transcript variant X21 XM_047448256.1:c. N/A Genic Upstream Transcript 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
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= T
GRCh38.p14 chr 1 NC_000001.11:g.3581819= NC_000001.11:g.3581819C>T
GRCh37.p13 chr 1 NC_000001.10:g.3498383= NC_000001.10:g.3498383C>T
MEGF6 transcript NM_001409.3:c.377-1890= NM_001409.3:c.377-1890G>A
MEGF6 transcript variant 1 NM_001409.4:c.377-1890= NM_001409.4:c.377-1890G>A
MEGF6 transcript variant X1 XM_011540886.3:c.563-1890= XM_011540886.3:c.563-1890G>A
MEGF6 transcript variant X15 XM_011540888.4:c.563-1890= XM_011540888.4:c.563-1890G>A
MEGF6 transcript variant X2 XM_017000533.3:c.563-1890= XM_017000533.3:c.563-1890G>A
MEGF6 transcript variant X3 XM_047448204.1:c.377-1890= XM_047448204.1:c.377-1890G>A
MEGF6 transcript variant X4 XM_047448205.1:c.377-1890= XM_047448205.1:c.377-1890G>A
MEGF6 transcript variant X5 XM_047448215.1:c.377-1890= XM_047448215.1:c.377-1890G>A
MEGF6 transcript variant X6 XM_047448217.1:c.377-1890= XM_047448217.1:c.377-1890G>A
MEGF6 transcript variant X7 XM_047448220.1:c.377-1890= XM_047448220.1:c.377-1890G>A
MEGF6 transcript variant X8 XM_047448221.1:c.377-1890= XM_047448221.1:c.377-1890G>A
MEGF6 transcript variant X9 XM_047448228.1:c.377-1890= XM_047448228.1:c.377-1890G>A
MEGF6 transcript variant X10 XM_047448229.1:c.377-1890= XM_047448229.1:c.377-1890G>A
MEGF6 transcript variant X11 XM_047448232.1:c.377-1890= XM_047448232.1:c.377-1890G>A
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#.

58 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss11375567 Jul 11, 2003 (116)
2 SC_SNP ss13395353 Dec 05, 2003 (119)
3 SI_EXO ss52081954 Oct 15, 2006 (127)
4 BCMHGSC_JDW ss87172823 Mar 23, 2008 (129)
5 BGI ss102714980 Dec 01, 2009 (131)
6 ENSEMBL ss137762631 Dec 01, 2009 (131)
7 GMI ss154557626 Dec 01, 2009 (131)
8 BUSHMAN ss197921489 Jul 04, 2010 (132)
9 BCM-HGSC-SUB ss205463864 Jul 04, 2010 (132)
10 1000GENOMES ss210454489 Jul 14, 2010 (132)
11 1000GENOMES ss218202050 Jul 14, 2010 (132)
12 1000GENOMES ss230403295 Jul 14, 2010 (132)
13 1000GENOMES ss238122255 Jul 15, 2010 (132)
14 GMI ss275690718 May 04, 2012 (137)
15 PJP ss290497898 May 09, 2011 (134)
16 TISHKOFF ss553732581 Apr 25, 2013 (138)
17 SSMP ss647534787 Apr 25, 2013 (138)
18 EVA-GONL ss974794085 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1067625895 Aug 21, 2014 (142)
20 1000GENOMES ss1289442979 Aug 21, 2014 (142)
21 DDI ss1425692218 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1573859252 Apr 01, 2015 (144)
23 EVA_DECODE ss1584153128 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1599423141 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1642417174 Apr 01, 2015 (144)
26 WEILL_CORNELL_DGM ss1917989513 Feb 12, 2016 (147)
27 GENOMED ss1966670927 Jul 19, 2016 (147)
28 JJLAB ss2019510895 Sep 14, 2016 (149)
29 USC_VALOUEV ss2147501224 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2159557251 Dec 20, 2016 (150)
31 GRF ss2697394965 Nov 08, 2017 (151)
32 GNOMAD ss2750949200 Nov 08, 2017 (151)
33 SWEGEN ss2986197954 Nov 08, 2017 (151)
34 BIOINF_KMB_FNS_UNIBA ss3023519072 Nov 08, 2017 (151)
35 CSHL ss3343287706 Nov 08, 2017 (151)
36 EGCUT_WGS ss3654299079 Jul 12, 2019 (153)
37 EVA_DECODE ss3686043012 Jul 12, 2019 (153)
38 ACPOP ss3726738126 Jul 12, 2019 (153)
39 EVA ss3745752436 Jul 12, 2019 (153)
40 KHV_HUMAN_GENOMES ss3798774120 Jul 12, 2019 (153)
41 EVA ss3825992964 Apr 25, 2020 (154)
42 SGDP_PRJ ss3848064401 Apr 25, 2020 (154)
43 KRGDB ss3892925296 Apr 25, 2020 (154)
44 KOGIC ss3943687858 Apr 25, 2020 (154)
45 TOPMED ss4437239612 Apr 25, 2021 (155)
46 TOMMO_GENOMICS ss5142191988 Apr 25, 2021 (155)
47 1000G_HIGH_COVERAGE ss5240960534 Oct 12, 2022 (156)
48 EVA ss5316359671 Oct 12, 2022 (156)
49 HUGCELL_USP ss5442187320 Oct 12, 2022 (156)
50 EVA ss5505751376 Oct 12, 2022 (156)
51 1000G_HIGH_COVERAGE ss5512623114 Oct 12, 2022 (156)
52 SANFORD_IMAGENETICS ss5624804067 Oct 12, 2022 (156)
53 TOMMO_GENOMICS ss5666402285 Oct 12, 2022 (156)
54 YY_MCH ss5800269663 Oct 12, 2022 (156)
55 EVA ss5831456464 Oct 12, 2022 (156)
56 EVA ss5848758197 Oct 12, 2022 (156)
57 EVA ss5906802247 Oct 12, 2022 (156)
58 EVA ss5936629057 Oct 12, 2022 (156)
59 1000Genomes NC_000001.10 - 3498383 Oct 11, 2018 (152)
60 1000Genomes_30x NC_000001.11 - 3581819 Oct 12, 2022 (156)
61 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3498383 Oct 11, 2018 (152)
62 Genetic variation in the Estonian population NC_000001.10 - 3498383 Oct 11, 2018 (152)
63 The Danish reference pan genome NC_000001.10 - 3498383 Apr 25, 2020 (154)
64 gnomAD - Genomes NC_000001.11 - 3581819 Apr 25, 2021 (155)
65 Genome of the Netherlands Release 5 NC_000001.10 - 3498383 Apr 25, 2020 (154)
66 KOREAN population from KRGDB NC_000001.10 - 3498383 Apr 25, 2020 (154)
67 Korean Genome Project NC_000001.11 - 3581819 Apr 25, 2020 (154)
68 Northern Sweden NC_000001.10 - 3498383 Jul 12, 2019 (153)
69 Qatari NC_000001.10 - 3498383 Apr 25, 2020 (154)
70 SGDP_PRJ NC_000001.10 - 3498383 Apr 25, 2020 (154)
71 Siberian NC_000001.10 - 3498383 Apr 25, 2020 (154)
72 8.3KJPN NC_000001.10 - 3498383 Apr 25, 2021 (155)
73 14KJPN NC_000001.11 - 3581819 Oct 12, 2022 (156)
74 TopMed NC_000001.11 - 3581819 Apr 25, 2021 (155)
75 UK 10K study - Twins NC_000001.10 - 3498383 Oct 11, 2018 (152)
76 ALFA NC_000001.11 - 3581819 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
ss87172823, ss197921489, ss205463864, ss210454489, ss275690718, ss290497898, ss1584153128 NC_000001.9:3488242:C:T NC_000001.11:3581818:C:T (self)
110727, 49034, 37327, 1366486, 21015, 102690, 22991, 31443, 81381, 17578, 161295, 49034, ss218202050, ss230403295, ss238122255, ss553732581, ss647534787, ss974794085, ss1067625895, ss1289442979, ss1425692218, ss1573859252, ss1599423141, ss1642417174, ss1917989513, ss1966670927, ss2019510895, ss2147501224, ss2697394965, ss2750949200, ss2986197954, ss3343287706, ss3654299079, ss3726738126, ss3745752436, ss3825992964, ss3848064401, ss3892925296, ss5142191988, ss5316359671, ss5505751376, ss5624804067, ss5831456464, ss5936629057 NC_000001.10:3498382:C:T NC_000001.11:3581818:C:T (self)
149049, 808350, 65859, 239389, 845947, 2835171290, ss2159557251, ss3023519072, ss3686043012, ss3798774120, ss3943687858, ss4437239612, ss5240960534, ss5442187320, ss5512623114, ss5666402285, ss5800269663, ss5848758197, ss5906802247 NC_000001.11:3581818:C:T NC_000001.11:3581818:C:T (self)
ss11375567 NT_004321.15:805157:C:T NC_000001.11:3581818:C:T (self)
ss52081954 NT_004321.16:805157:C:T NC_000001.11:3581818:C:T (self)
ss13395353, ss102714980, ss137762631, ss154557626 NT_004350.19:2977014:C:T NC_000001.11:3581818: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 rs7528821

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.post761+d5e8e07