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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs477591

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:5967935 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.028331 (7499/264690, TOPMED)
G=0.025472 (3573/140270, GnomAD)
G=0.02256 (358/15872, ALFA) (+ 9 more)
G=0.0298 (191/6404, 1000G_30x)
G=0.0276 (138/5008, 1000G)
G=0.0010 (4/3854, ALSPAC)
G=0.0011 (4/3708, TWINSUK)
G=0.0178 (37/2084, HGDP_Stanford)
G=0.0674 (86/1276, HapMap)
G=0.014 (3/216, Qatari)
G=0.020 (2/102, Ancient Sardinia)
A=0.41 (9/22, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
L3MBTL4 : Intron Variant
LOC121725015 : 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 15872 A=0.97744 G=0.02256
European Sub 9832 A=0.9978 G=0.0022
African Sub 4082 A=0.9228 G=0.0772
African Others Sub 144 A=0.917 G=0.083
African American Sub 3938 A=0.9231 G=0.0769
Asian Sub 116 A=1.000 G=0.000
East Asian Sub 88 A=1.00 G=0.00
Other Asian Sub 28 A=1.00 G=0.00
Latin American 1 Sub 154 A=0.981 G=0.019
Latin American 2 Sub 616 A=0.992 G=0.008
South Asian Sub 98 A=1.00 G=0.00
Other Sub 974 A=0.987 G=0.013


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=0.971669 G=0.028331
gnomAD - Genomes Global Study-wide 140270 A=0.974528 G=0.025472
gnomAD - Genomes European Sub 75966 A=0.99901 G=0.00099
gnomAD - Genomes African Sub 42034 A=0.92299 G=0.07701
gnomAD - Genomes American Sub 13664 A=0.98734 G=0.01266
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.9904 G=0.0096
gnomAD - Genomes East Asian Sub 3130 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 A=0.9740 G=0.0260
Allele Frequency Aggregator Total Global 15872 A=0.97744 G=0.02256
Allele Frequency Aggregator European Sub 9832 A=0.9978 G=0.0022
Allele Frequency Aggregator African Sub 4082 A=0.9228 G=0.0772
Allele Frequency Aggregator Other Sub 974 A=0.987 G=0.013
Allele Frequency Aggregator Latin American 2 Sub 616 A=0.992 G=0.008
Allele Frequency Aggregator Latin American 1 Sub 154 A=0.981 G=0.019
Allele Frequency Aggregator Asian Sub 116 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
1000Genomes_30x Global Study-wide 6404 A=0.9702 G=0.0298
1000Genomes_30x African Sub 1786 A=0.9099 G=0.0901
1000Genomes_30x Europe Sub 1266 A=0.9984 G=0.0016
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.971 G=0.029
1000Genomes Global Study-wide 5008 A=0.9724 G=0.0276
1000Genomes African Sub 1322 A=0.9115 G=0.0885
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9980 G=0.0020
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.973 G=0.027
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9990 G=0.0010
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9989 G=0.0011
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 A=0.9822 G=0.0178
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 A=0.966 G=0.034
HGDP-CEPH-db Supplement 1 Europe Sub 320 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Africa Sub 242 A=0.897 G=0.103
HGDP-CEPH-db Supplement 1 America Sub 216 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 A=1.00 G=0.00
HapMap Global Study-wide 1276 A=0.9326 G=0.0674
HapMap African Sub 692 A=0.900 G=0.100
HapMap American Sub 318 A=0.950 G=0.050
HapMap Europe Sub 176 A=0.994 G=0.006
HapMap Asian Sub 90 A=1.00 G=0.00
Qatari Global Study-wide 216 A=0.986 G=0.014
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 102 A=0.980 G=0.020
SGDP_PRJ Global Study-wide 22 A=0.41 G=0.59
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 18 NC_000018.10:g.5967935A>G
GRCh37.p13 chr 18 NC_000018.9:g.5967934A>G
Gene: L3MBTL4, L3MBTL histone methyl-lysine binding protein 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
L3MBTL4 transcript variant 2 NM_001330559.2:c.1614+145…

NM_001330559.2:c.1614+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant 3 NM_001365765.2:c.1614+145…

NM_001365765.2:c.1614+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant 8 NM_001365768.2:c.1374-777…

NM_001365768.2:c.1374-7779T>C

 		N/A Intron Variant
L3MBTL4 transcript variant 9 NM_001365769.2:c.1374-777…

NM_001365769.2:c.1374-7779T>C

 		N/A Intron Variant
L3MBTL4 transcript variant 10 NM_001365770.2:c.1641+145…

NM_001365770.2:c.1641+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant 1 NM_173464.4:c.1641+1458T>C N/A Intron Variant
L3MBTL4 transcript variant 6 NM_001365766.2:c. N/A Genic Downstream Transcript Variant
L3MBTL4 transcript variant 7 NM_001365767.2:c. N/A Genic Downstream Transcript Variant
L3MBTL4 transcript variant 4 NR_158609.2:n. N/A Intron Variant
L3MBTL4 transcript variant 5 NR_158610.2:n. N/A Intron Variant
L3MBTL4 transcript variant 11 NR_158611.2:n. N/A Intron Variant
L3MBTL4 transcript variant X1 XM_011525757.2:c.1641+145…

XM_011525757.2:c.1641+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X3 XM_011525758.2:c.1641+145…

XM_011525758.2:c.1641+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X6 XM_011525759.2:c.1641+145…

XM_011525759.2:c.1641+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X7 XM_011525760.2:c.1614+145…

XM_011525760.2:c.1614+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X20 XM_011525767.3:c.774+1458…

XM_011525767.3:c.774+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X11 XM_017026074.2:c.1374-777…

XM_017026074.2:c.1374-7779T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X2 XM_047437914.1:c.1641+145…

XM_047437914.1:c.1641+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X4 XM_047437915.1:c.1641+145…

XM_047437915.1:c.1641+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X5 XM_047437916.1:c.1641+145…

XM_047437916.1:c.1641+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X8 XM_047437917.1:c.1614+145…

XM_047437917.1:c.1614+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X9 XM_047437918.1:c.1614+145…

XM_047437918.1:c.1614+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X10 XM_047437919.1:c.1614+145…

XM_047437919.1:c.1614+1458T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X14 XM_047437920.1:c.1374-777…

XM_047437920.1:c.1374-7779T>C

 		N/A Intron Variant
L3MBTL4 transcript variant X15 XM_006722364.3:c. N/A Genic Downstream Transcript Variant
L3MBTL4 transcript variant X12 XM_011525762.3:c. N/A Genic Downstream Transcript Variant
L3MBTL4 transcript variant X13 XM_011525763.3:c. N/A Genic Downstream Transcript Variant
L3MBTL4 transcript variant X18 XM_017026077.2:c. N/A Genic Downstream Transcript Variant
L3MBTL4 transcript variant X16 XR_007066252.1:n. N/A Genic Downstream Transcript Variant
L3MBTL4 transcript variant X17 XR_007066253.1:n. N/A Genic Downstream Transcript Variant
L3MBTL4 transcript variant X19 XR_935072.2:n. N/A Genic Downstream Transcript Variant
Gene: LOC121725015, uncharacterized LOC121725015 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC121725015 transcript variant 1 NR_172504.1:n. N/A Intron Variant
LOC121725015 transcript variant 2 NR_172505.1:n. 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
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= G
GRCh38.p14 chr 18 NC_000018.10:g.5967935= NC_000018.10:g.5967935A>G
GRCh37.p13 chr 18 NC_000018.9:g.5967934= NC_000018.9:g.5967934A>G
L3MBTL4 transcript variant 2 NM_001330559.2:c.1614+1458= NM_001330559.2:c.1614+1458T>C
L3MBTL4 transcript variant 3 NM_001365765.2:c.1614+1458= NM_001365765.2:c.1614+1458T>C
L3MBTL4 transcript variant 8 NM_001365768.2:c.1374-7779= NM_001365768.2:c.1374-7779T>C
L3MBTL4 transcript variant 9 NM_001365769.2:c.1374-7779= NM_001365769.2:c.1374-7779T>C
L3MBTL4 transcript variant 10 NM_001365770.2:c.1641+1458= NM_001365770.2:c.1641+1458T>C
L3MBTL4 transcript variant 1 NM_173464.3:c.1641+1458= NM_173464.3:c.1641+1458T>C
L3MBTL4 transcript variant 1 NM_173464.4:c.1641+1458= NM_173464.4:c.1641+1458T>C
L3MBTL4 transcript variant X1 XM_005258165.1:c.1641+1458= XM_005258165.1:c.1641+1458T>C
L3MBTL4 transcript variant X6 XM_005258166.1:c.1614+1458= XM_005258166.1:c.1614+1458T>C
L3MBTL4 transcript variant X3 XM_005258167.1:c.1614+1458= XM_005258167.1:c.1614+1458T>C
L3MBTL4 transcript variant X5 XM_005258169.1:c.*40+1458= XM_005258169.1:c.*40+1458T>C
L3MBTL4 transcript variant X1 XM_011525757.2:c.1641+1458= XM_011525757.2:c.1641+1458T>C
L3MBTL4 transcript variant X3 XM_011525758.2:c.1641+1458= XM_011525758.2:c.1641+1458T>C
L3MBTL4 transcript variant X6 XM_011525759.2:c.1641+1458= XM_011525759.2:c.1641+1458T>C
L3MBTL4 transcript variant X7 XM_011525760.2:c.1614+1458= XM_011525760.2:c.1614+1458T>C
L3MBTL4 transcript variant X20 XM_011525767.3:c.774+1458= XM_011525767.3:c.774+1458T>C
L3MBTL4 transcript variant X11 XM_017026074.2:c.1374-7779= XM_017026074.2:c.1374-7779T>C
L3MBTL4 transcript variant X2 XM_047437914.1:c.1641+1458= XM_047437914.1:c.1641+1458T>C
L3MBTL4 transcript variant X4 XM_047437915.1:c.1641+1458= XM_047437915.1:c.1641+1458T>C
L3MBTL4 transcript variant X5 XM_047437916.1:c.1641+1458= XM_047437916.1:c.1641+1458T>C
L3MBTL4 transcript variant X8 XM_047437917.1:c.1614+1458= XM_047437917.1:c.1614+1458T>C
L3MBTL4 transcript variant X9 XM_047437918.1:c.1614+1458= XM_047437918.1:c.1614+1458T>C
L3MBTL4 transcript variant X10 XM_047437919.1:c.1614+1458= XM_047437919.1:c.1614+1458T>C
L3MBTL4 transcript variant X14 XM_047437920.1:c.1374-7779= XM_047437920.1:c.1374-7779T>C
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#.

39 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss647078 Aug 11, 2000 (83)
2 TSC-CSHL ss2774620 Jan 22, 2001 (92)
3 BCM_SSAHASNP ss10893871 Jul 11, 2003 (116)
4 ILLUMINA ss67755540 Nov 30, 2006 (127)
5 ILLUMINA ss71405779 May 17, 2007 (127)
6 ILLUMINA ss75373342 Dec 07, 2007 (129)
7 1000GENOMES ss114007262 Jan 25, 2009 (130)
8 KRIBB_YJKIM ss119354893 Dec 01, 2009 (131)
9 COMPLETE_GENOMICS ss168985718 Jul 04, 2010 (132)
10 ILLUMINA ss173807999 Jul 04, 2010 (132)
11 1000GENOMES ss227720091 Jul 14, 2010 (132)
12 ILLUMINA ss537272418 Sep 08, 2015 (146)
13 JMKIDD_LAB ss1081301189 Aug 21, 2014 (142)
14 1000GENOMES ss1359989407 Aug 21, 2014 (142)
15 DDI ss1428134932 Apr 01, 2015 (144)
16 EVA_UK10K_ALSPAC ss1636335355 Apr 01, 2015 (144)
17 EVA_UK10K_TWINSUK ss1679329388 Apr 01, 2015 (144)
18 WEILL_CORNELL_DGM ss1936925148 Feb 12, 2016 (147)
19 HUMAN_LONGEVITY ss2219539588 Dec 20, 2016 (150)
20 GNOMAD ss2953721279 Nov 08, 2017 (151)
21 SWEGEN ss3016100054 Nov 08, 2017 (151)
22 ILLUMINA ss3627752140 Oct 12, 2018 (152)
23 ILLUMINA ss3638181647 Oct 12, 2018 (152)
24 ILLUMINA ss3643158405 Oct 12, 2018 (152)
25 EVA_DECODE ss3701149632 Jul 13, 2019 (153)
26 KHV_HUMAN_GENOMES ss3820340281 Jul 13, 2019 (153)
27 HGDP ss3847574486 Apr 27, 2020 (154)
28 SGDP_PRJ ss3886472242 Apr 27, 2020 (154)
29 EVA ss3985810225 Apr 27, 2021 (155)
30 EVA ss4017784532 Apr 27, 2021 (155)
31 TOPMED ss5047530618 Apr 27, 2021 (155)
32 1000G_HIGH_COVERAGE ss5304346234 Oct 16, 2022 (156)
33 EVA ss5429757741 Oct 16, 2022 (156)
34 HUGCELL_USP ss5497264323 Oct 16, 2022 (156)
35 1000G_HIGH_COVERAGE ss5608622739 Oct 16, 2022 (156)
36 SANFORD_IMAGENETICS ss5660775265 Oct 16, 2022 (156)
37 EVA ss5827191432 Oct 16, 2022 (156)
38 EVA ss5873056778 Oct 16, 2022 (156)
39 EVA ss5952175151 Oct 16, 2022 (156)
40 1000Genomes NC_000018.9 - 5967934 Oct 12, 2018 (152)
41 1000Genomes_30x NC_000018.10 - 5967935 Oct 16, 2022 (156)
42 The Avon Longitudinal Study of Parents and Children NC_000018.9 - 5967934 Oct 12, 2018 (152)
43 gnomAD - Genomes NC_000018.10 - 5967935 Apr 27, 2021 (155)
44 HGDP-CEPH-db Supplement 1 NC_000018.8 - 5957934 Apr 27, 2020 (154)
45 HapMap NC_000018.10 - 5967935 Apr 27, 2020 (154)
46 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000018.9 - 5967934 Apr 27, 2021 (155)
47 Qatari NC_000018.9 - 5967934 Apr 27, 2020 (154)
48 SGDP_PRJ NC_000018.9 - 5967934 Apr 27, 2020 (154)
49 TopMed NC_000018.10 - 5967935 Apr 27, 2021 (155)
50 UK 10K study - Twins NC_000018.9 - 5967934 Oct 12, 2018 (152)
51 ALFA NC_000018.10 - 5967935 Apr 27, 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
252378, ss114007262, ss168985718, ss3643158405, ss3847574486 NC_000018.8:5957933:A:G NC_000018.10:5967934:A:G (self)
73282204, 40605738, 1036152, 18967070, 38489222, 40605738, ss227720091, ss537272418, ss1081301189, ss1359989407, ss1428134932, ss1636335355, ss1679329388, ss1936925148, ss2953721279, ss3016100054, ss3627752140, ss3638181647, ss3886472242, ss3985810225, ss4017784532, ss5429757741, ss5660775265, ss5827191432, ss5952175151 NC_000018.9:5967933:A:G NC_000018.10:5967934:A:G (self)
96148674, 517033424, 1546507, 263076281, 13162906868, ss2219539588, ss3701149632, ss3820340281, ss5047530618, ss5304346234, ss5497264323, ss5608622739, ss5873056778 NC_000018.10:5967934:A:G NC_000018.10:5967934:A:G (self)
ss10893871 NT_010859.12:5957935:A:G NC_000018.10:5967934:A:G (self)
ss647078, ss2774620, ss67755540, ss71405779, ss75373342, ss119354893, ss173807999 NT_010859.14:5957933:A:G NC_000018.10:5967934:A:G (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 rs477591

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