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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.

rs61736594

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:65169932 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.067857 (17961/264690, TOPMED)
T=0.068518 (9598/140080, GnomAD)
T=0.06838 (3903/57082, ALFA) (+ 17 more)
T=0.08955 (4451/49706, GnomAD_exome)
T=0.16013 (4525/28258, 14KJPN)
T=0.16056 (2691/16760, 8.3KJPN)
T=0.0826 (529/6404, 1000G_30x)
T=0.0833 (417/5008, 1000G)
T=0.0772 (346/4480, Estonian)
T=0.0638 (246/3854, ALSPAC)
T=0.0677 (251/3708, TWINSUK)
T=0.1737 (508/2924, KOREAN)
T=0.141 (112/792, PRJEB37584)
T=0.098 (59/600, NorthernSweden)
T=0.203 (70/344, ExAC)
T=0.079 (17/216, Qatari)
T=0.194 (42/216, Vietnamese)
C=0.483 (57/118, SGDP_PRJ)
T=0.05 (2/40, GENOME_DK)
C=0.46 (11/24, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
LEMD3 : Synonymous Variant
LOC124902953 : 2KB Upstream 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 57204 C=0.93167 T=0.06833
European Sub 49700 C=0.93000 T=0.07000
African Sub 3160 C=0.9677 T=0.0323
African Others Sub 118 C=0.983 T=0.017
African American Sub 3042 C=0.9671 T=0.0329
Asian Sub 160 C=0.856 T=0.144
East Asian Sub 98 C=0.88 T=0.12
Other Asian Sub 62 C=0.82 T=0.18
Latin American 1 Sub 146 C=0.904 T=0.096
Latin American 2 Sub 630 C=0.892 T=0.108
South Asian Sub 98 C=0.92 T=0.08
Other Sub 3310 C=0.9350 T=0.0650


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=0.932143 T=0.067857
gnomAD - Genomes Global Study-wide 140080 C=0.931482 T=0.068518
gnomAD - Genomes European Sub 75824 C=0.92273 T=0.07727
gnomAD - Genomes African Sub 42016 C=0.96511 T=0.03489
gnomAD - Genomes American Sub 13646 C=0.90613 T=0.09387
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.8925 T=0.1075
gnomAD - Genomes East Asian Sub 3118 C=0.8566 T=0.1434
gnomAD - Genomes Other Sub 2154 C=0.9127 T=0.0873
Allele Frequency Aggregator Total Global 57082 C=0.93162 T=0.06838
Allele Frequency Aggregator European Sub 49596 C=0.92997 T=0.07003
Allele Frequency Aggregator Other Sub 3306 C=0.9350 T=0.0650
Allele Frequency Aggregator African Sub 3146 C=0.9676 T=0.0324
Allele Frequency Aggregator Latin American 2 Sub 630 C=0.892 T=0.108
Allele Frequency Aggregator Asian Sub 160 C=0.856 T=0.144
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.904 T=0.096
Allele Frequency Aggregator South Asian Sub 98 C=0.92 T=0.08
gnomAD - Exomes Global Study-wide 49706 C=0.91045 T=0.08955
gnomAD - Exomes European Sub 24794 C=0.91796 T=0.08204
gnomAD - Exomes Asian Sub 11370 C=0.89129 T=0.10871
gnomAD - Exomes American Sub 8568 C=0.8960 T=0.1040
gnomAD - Exomes African Sub 2342 C=0.9658 T=0.0342
gnomAD - Exomes Other Sub 1534 C=0.9342 T=0.0658
gnomAD - Exomes Ashkenazi Jewish Sub 1098 C=0.9007 T=0.0993
14KJPN JAPANESE Study-wide 28258 C=0.83987 T=0.16013
8.3KJPN JAPANESE Study-wide 16760 C=0.83944 T=0.16056
1000Genomes_30x Global Study-wide 6404 C=0.9174 T=0.0826
1000Genomes_30x African Sub 1786 C=0.9832 T=0.0168
1000Genomes_30x Europe Sub 1266 C=0.9179 T=0.0821
1000Genomes_30x South Asian Sub 1202 C=0.9060 T=0.0940
1000Genomes_30x East Asian Sub 1170 C=0.8436 T=0.1564
1000Genomes_30x American Sub 980 C=0.899 T=0.101
1000Genomes Global Study-wide 5008 C=0.9167 T=0.0833
1000Genomes African Sub 1322 C=0.9803 T=0.0197
1000Genomes East Asian Sub 1008 C=0.8472 T=0.1528
1000Genomes Europe Sub 1006 C=0.9215 T=0.0785
1000Genomes South Asian Sub 978 C=0.909 T=0.091
1000Genomes American Sub 694 C=0.901 T=0.099
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9228 T=0.0772
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9362 T=0.0638
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9323 T=0.0677
KOREAN population from KRGDB KOREAN Study-wide 2924 C=0.8263 G=0.0000, T=0.1737
CNV burdens in cranial meningiomas Global Study-wide 792 C=0.859 T=0.141
CNV burdens in cranial meningiomas CRM Sub 792 C=0.859 T=0.141
Northern Sweden ACPOP Study-wide 600 C=0.902 T=0.098
ExAC Global Study-wide 344 C=0.797 T=0.203
ExAC Asian Sub 198 C=0.773 T=0.227
ExAC Europe Sub 118 C=0.822 T=0.178
ExAC American Sub 12 C=0.67 T=0.33
ExAC African Sub 10 C=1.0 T=0.0
ExAC Other Sub 6 C=1.0 T=0.0
Qatari Global Study-wide 216 C=0.921 T=0.079
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.806 T=0.194
SGDP_PRJ Global Study-wide 118 C=0.483 T=0.517
The Danish reference pan genome Danish Study-wide 40 C=0.95 T=0.05
Siberian Global Study-wide 24 C=0.46 T=0.54
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 12 NC_000012.12:g.65169932C>G
GRCh38.p14 chr 12 NC_000012.12:g.65169932C>T
GRCh37.p13 chr 12 NC_000012.11:g.65563712C>G
GRCh37.p13 chr 12 NC_000012.11:g.65563712C>T
LEMD3 RefSeqGene NG_016210.2:g.5362C>G
LEMD3 RefSeqGene NG_016210.2:g.5362C>T
Gene: LEMD3, LEM domain containing 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LEMD3 transcript variant 1 NM_014319.5:c.336C>G A [GCC] > A [GCG] Coding Sequence Variant
inner nuclear membrane protein Man1 isoform 1 NP_055134.2:p.Ala112= A (Ala) > A (Ala) Synonymous Variant
LEMD3 transcript variant 1 NM_014319.5:c.336C>T A [GCC] > A [GCT] Coding Sequence Variant
inner nuclear membrane protein Man1 isoform 1 NP_055134.2:p.Ala112= A (Ala) > A (Ala) Synonymous Variant
LEMD3 transcript variant 2 NM_001167614.2:c.336C>G A [GCC] > A [GCG] Coding Sequence Variant
inner nuclear membrane protein Man1 isoform 2 NP_001161086.1:p.Ala112= A (Ala) > A (Ala) Synonymous Variant
LEMD3 transcript variant 2 NM_001167614.2:c.336C>T A [GCC] > A [GCT] Coding Sequence Variant
inner nuclear membrane protein Man1 isoform 2 NP_001161086.1:p.Ala112= A (Ala) > A (Ala) Synonymous Variant
Gene: LOC124902953, uncharacterized LOC124902953 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC124902953 transcript XR_007063349.1:n. N/A 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.

Allele: T (allele ID: 326356 )
ClinVar Accession Disease Names Clinical Significance
RCV000332026.3 Dermatofibrosis lenticularis disseminata Benign
RCV000595761.3 not specified Benign
RCV001513962.6 not provided Benign
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= G T
GRCh38.p14 chr 12 NC_000012.12:g.65169932= NC_000012.12:g.65169932C>G NC_000012.12:g.65169932C>T
GRCh37.p13 chr 12 NC_000012.11:g.65563712= NC_000012.11:g.65563712C>G NC_000012.11:g.65563712C>T
LEMD3 RefSeqGene NG_016210.2:g.5362= NG_016210.2:g.5362C>G NG_016210.2:g.5362C>T
LEMD3 transcript variant 1 NM_014319.5:c.336= NM_014319.5:c.336C>G NM_014319.5:c.336C>T
LEMD3 transcript variant 1 NM_014319.4:c.336= NM_014319.4:c.336C>G NM_014319.4:c.336C>T
LEMD3 transcript variant 2 NM_001167614.2:c.336= NM_001167614.2:c.336C>G NM_001167614.2:c.336C>T
LEMD3 transcript variant 2 NM_001167614.1:c.336= NM_001167614.1:c.336C>G NM_001167614.1:c.336C>T
inner nuclear membrane protein Man1 isoform 1 NP_055134.2:p.Ala112= NP_055134.2:p.Ala112= NP_055134.2:p.Ala112=
inner nuclear membrane protein Man1 isoform 2 NP_001161086.1:p.Ala112= NP_001161086.1:p.Ala112= NP_001161086.1:p.Ala112=
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#.

72 SubSNP, 20 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CORNELL ss86243590 Mar 23, 2008 (129)
2 COMPLETE_GENOMICS ss175160105 Jul 04, 2010 (132)
3 1000GENOMES ss242521397 Jul 15, 2010 (132)
4 EXOME_CHIP ss491470588 May 04, 2012 (137)
5 TISHKOFF ss563219271 Apr 25, 2013 (138)
6 SSMP ss658783671 Apr 25, 2013 (138)
7 ILLUMINA ss783473138 Sep 08, 2015 (146)
8 EVA-GONL ss989629408 Aug 21, 2014 (142)
9 JMKIDD_LAB ss1078528880 Aug 21, 2014 (142)
10 1000GENOMES ss1345388659 Aug 21, 2014 (142)
11 EVA_GENOME_DK ss1576335651 Apr 01, 2015 (144)
12 EVA_DECODE ss1599305604 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1628780952 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1671774985 Apr 01, 2015 (144)
15 EVA_EXAC ss1691001006 Apr 01, 2015 (144)
16 ILLUMINA ss1752077304 Sep 08, 2015 (146)
17 ILLUMINA ss1917876005 Feb 12, 2016 (147)
18 WEILL_CORNELL_DGM ss1932993534 Feb 12, 2016 (147)
19 ILLUMINA ss1946342354 Feb 12, 2016 (147)
20 ILLUMINA ss1959443333 Feb 12, 2016 (147)
21 JJLAB ss2027246205 Sep 14, 2016 (149)
22 USC_VALOUEV ss2155588976 Dec 20, 2016 (150)
23 HUMAN_LONGEVITY ss2190549212 Dec 20, 2016 (150)
24 SYSTEMSBIOZJU ss2628105884 Nov 08, 2017 (151)
25 GRF ss2699937835 Nov 08, 2017 (151)
26 GNOMAD ss2739960817 Nov 08, 2017 (151)
27 GNOMAD ss2748909628 Nov 08, 2017 (151)
28 GNOMAD ss2911592337 Nov 08, 2017 (151)
29 SWEGEN ss3009843609 Nov 08, 2017 (151)
30 ILLUMINA ss3021440248 Nov 08, 2017 (151)
31 CSHL ss3350106475 Nov 08, 2017 (151)
32 ILLUMINA ss3634509870 Oct 12, 2018 (152)
33 ILLUMINA ss3640217203 Oct 12, 2018 (152)
34 ILLUMINA ss3644595330 Oct 12, 2018 (152)
35 BIOINF_KMB_FNS_UNIBA ss3645257946 Oct 12, 2018 (152)
36 URBANLAB ss3649858158 Oct 12, 2018 (152)
37 ILLUMINA ss3651820491 Oct 12, 2018 (152)
38 EGCUT_WGS ss3677111451 Jul 13, 2019 (153)
39 EVA_DECODE ss3693853011 Jul 13, 2019 (153)
40 ACPOP ss3739102700 Jul 13, 2019 (153)
41 ILLUMINA ss3744398074 Jul 13, 2019 (153)
42 ILLUMINA ss3744810548 Jul 13, 2019 (153)
43 EVA ss3750590923 Jul 13, 2019 (153)
44 ILLUMINA ss3772309963 Jul 13, 2019 (153)
45 KHV_HUMAN_GENOMES ss3815923182 Jul 13, 2019 (153)
46 EVA ss3825824560 Apr 27, 2020 (154)
47 EVA ss3833168446 Apr 27, 2020 (154)
48 EVA ss3840154334 Apr 27, 2020 (154)
49 EVA ss3845641279 Apr 27, 2020 (154)
50 SGDP_PRJ ss3878469072 Apr 27, 2020 (154)
51 KRGDB ss3927132004 Apr 27, 2020 (154)
52 FSA-LAB ss3984031870 Apr 26, 2021 (155)
53 EVA ss3984668363 Apr 26, 2021 (155)
54 EVA ss3986576525 Apr 26, 2021 (155)
55 TOPMED ss4921615412 Apr 26, 2021 (155)
56 TOMMO_GENOMICS ss5206754076 Apr 26, 2021 (155)
57 EVA ss5236907252 Apr 26, 2021 (155)
58 1000G_HIGH_COVERAGE ss5291139873 Oct 16, 2022 (156)
59 TRAN_CS_UWATERLOO ss5314436029 Oct 16, 2022 (156)
60 EVA ss5406232377 Oct 16, 2022 (156)
61 HUGCELL_USP ss5485851199 Oct 16, 2022 (156)
62 1000G_HIGH_COVERAGE ss5588793423 Oct 16, 2022 (156)
63 EVA ss5624034145 Oct 16, 2022 (156)
64 SANFORD_IMAGENETICS ss5653339105 Oct 16, 2022 (156)
65 TOMMO_GENOMICS ss5756675114 Oct 16, 2022 (156)
66 YY_MCH ss5813379755 Oct 16, 2022 (156)
67 EVA ss5838091286 Oct 16, 2022 (156)
68 EVA ss5847673865 Oct 16, 2022 (156)
69 EVA ss5848356406 Oct 16, 2022 (156)
70 EVA ss5850419341 Oct 16, 2022 (156)
71 EVA ss5904761890 Oct 16, 2022 (156)
72 EVA ss5944707222 Oct 16, 2022 (156)
73 1000Genomes NC_000012.11 - 65563712 Oct 12, 2018 (152)
74 1000Genomes_30x NC_000012.12 - 65169932 Oct 16, 2022 (156)
75 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 65563712 Oct 12, 2018 (152)
76 Genetic variation in the Estonian population NC_000012.11 - 65563712 Oct 12, 2018 (152)
77 ExAC NC_000012.11 - 65563712 Oct 12, 2018 (152)
78 The Danish reference pan genome NC_000012.11 - 65563712 Apr 27, 2020 (154)
79 gnomAD - Genomes NC_000012.12 - 65169932 Apr 26, 2021 (155)
80 gnomAD - Exomes NC_000012.11 - 65563712 Jul 13, 2019 (153)
81 KOREAN population from KRGDB NC_000012.11 - 65563712 Apr 27, 2020 (154)
82 Northern Sweden NC_000012.11 - 65563712 Jul 13, 2019 (153)
83 CNV burdens in cranial meningiomas NC_000012.11 - 65563712 Apr 26, 2021 (155)
84 Qatari NC_000012.11 - 65563712 Apr 27, 2020 (154)
85 SGDP_PRJ NC_000012.11 - 65563712 Apr 27, 2020 (154)
86 Siberian NC_000012.11 - 65563712 Apr 27, 2020 (154)
87 8.3KJPN NC_000012.11 - 65563712 Apr 26, 2021 (155)
88 14KJPN NC_000012.12 - 65169932 Oct 16, 2022 (156)
89 TopMed NC_000012.12 - 65169932 Apr 26, 2021 (155)
90 UK 10K study - Twins NC_000012.11 - 65563712 Oct 12, 2018 (152)
91 A Vietnamese Genetic Variation Database NC_000012.11 - 65563712 Jul 13, 2019 (153)
92 ALFA NC_000012.12 - 65169932 Apr 26, 2021 (155)
93 ClinVar RCV000332026.3 Oct 16, 2022 (156)
94 ClinVar RCV000595761.3 Oct 16, 2022 (156)
95 ClinVar RCV001513962.6 Oct 16, 2022 (156)
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
34309398, ss3927132004 NC_000012.11:65563711:C:G NC_000012.12:65169931:C:G (self)
ss175160105, ss1599305604 NC_000012.10:63849978:C:T NC_000012.12:65169931:C:T (self)
58151389, 32284810, 22849699, 1305155, 2999357, 9195574, 34309398, 12387565, 217856, 15035464, 30486052, 8105330, 64723383, 32284810, 7165937, ss242521397, ss491470588, ss563219271, ss658783671, ss783473138, ss989629408, ss1078528880, ss1345388659, ss1576335651, ss1628780952, ss1671774985, ss1691001006, ss1752077304, ss1917876005, ss1932993534, ss1946342354, ss1959443333, ss2027246205, ss2155588976, ss2628105884, ss2699937835, ss2739960817, ss2748909628, ss2911592337, ss3009843609, ss3021440248, ss3350106475, ss3634509870, ss3640217203, ss3644595330, ss3651820491, ss3677111451, ss3739102700, ss3744398074, ss3744810548, ss3750590923, ss3772309963, ss3825824560, ss3833168446, ss3840154334, ss3878469072, ss3927132004, ss3984031870, ss3984668363, ss3986576525, ss5206754076, ss5406232377, ss5624034145, ss5653339105, ss5838091286, ss5847673865, ss5848356406, ss5944707222 NC_000012.11:65563711:C:T NC_000012.12:65169931:C:T (self)
RCV000332026.3, RCV000595761.3, RCV001513962.6, 76319358, 410105690, 90512218, 137161069, 8128693790, ss2190549212, ss3645257946, ss3649858158, ss3693853011, ss3815923182, ss3845641279, ss4921615412, ss5236907252, ss5291139873, ss5314436029, ss5485851199, ss5588793423, ss5756675114, ss5813379755, ss5850419341, ss5904761890 NC_000012.12:65169931:C:T NC_000012.12:65169931:C:T (self)
ss86243590 NT_029419.12:27707017:C:T NC_000012.12:65169931: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 rs61736594

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