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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.

rs183253527

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:65170544 (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=0.001194 (299/250366, GnomAD_exome)
T=0.000471 (66/140208, GnomAD)
T=0.001255 (150/119516, ExAC) (+ 11 more)
T=0.01695 (479/28258, 14KJPN)
T=0.00009 (2/23404, ALFA)
T=0.01796 (301/16760, 8.3KJPN)
T=0.00008 (1/13006, GO-ESP)
T=0.0027 (17/6404, 1000G_30x)
T=0.0032 (16/5008, 1000G)
T=0.0206 (60/2918, KOREAN)
T=0.0207 (38/1832, Korea1K)
T=0.013 (8/614, Vietnamese)
C=0.5 (3/6, SGDP_PRJ)
T=0.5 (3/6, SGDP_PRJ)
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 23404 C=0.99991 G=0.00000, T=0.00009
European Sub 15886 C=1.00000 G=0.00000, T=0.00000
African Sub 3540 C=1.0000 G=0.0000, T=0.0000
African Others Sub 122 C=1.000 G=0.000, T=0.000
African American Sub 3418 C=1.0000 G=0.0000, T=0.0000
Asian Sub 164 C=0.988 G=0.000, T=0.012
East Asian Sub 108 C=0.991 G=0.000, T=0.009
Other Asian Sub 56 C=0.98 G=0.00, T=0.02
Latin American 1 Sub 146 C=1.000 G=0.000, T=0.000
Latin American 2 Sub 610 C=1.000 G=0.000, T=0.000
South Asian Sub 98 C=1.00 G=0.00, T=0.00
Other Sub 2960 C=1.0000 G=0.0000, T=0.0000


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
gnomAD - Exomes Global Study-wide 250366 C=0.998806 T=0.001194
gnomAD - Exomes European Sub 134712 C=0.999985 T=0.000015
gnomAD - Exomes Asian Sub 48982 C=0.99398 T=0.00602
gnomAD - Exomes American Sub 34538 C=0.99994 T=0.00006
gnomAD - Exomes African Sub 15976 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10054 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6104 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140208 C=0.999529 T=0.000471
gnomAD - Genomes European Sub 75928 C=0.99997 T=0.00003
gnomAD - Genomes African Sub 42030 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13642 C=0.99993 T=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=0.9805 T=0.0195
gnomAD - Genomes Other Sub 2154 C=0.9991 T=0.0009
ExAC Global Study-wide 119516 C=0.998745 T=0.001255
ExAC Europe Sub 72200 C=0.99999 T=0.00001
ExAC Asian Sub 25090 C=0.99414 T=0.00586
ExAC American Sub 11502 C=0.99991 T=0.00009
ExAC African Sub 9838 C=1.0000 T=0.0000
ExAC Other Sub 886 C=0.999 T=0.001
14KJPN JAPANESE Study-wide 28258 C=0.98305 T=0.01695
Allele Frequency Aggregator Total Global 23404 C=0.99991 G=0.00000, T=0.00009
Allele Frequency Aggregator European Sub 15886 C=1.00000 G=0.00000, T=0.00000
Allele Frequency Aggregator African Sub 3540 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 2960 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 164 C=0.988 G=0.000, T=0.012
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 G=0.00, T=0.00
8.3KJPN JAPANESE Study-wide 16760 C=0.98204 T=0.01796
GO Exome Sequencing Project Global Study-wide 13006 C=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8600 C=0.9999 T=0.0001
GO Exome Sequencing Project African American Sub 4406 C=1.0000 T=0.0000
1000Genomes_30x Global Study-wide 6404 C=0.9973 T=0.0027
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=0.9992 T=0.0008
1000Genomes_30x East Asian Sub 1170 C=0.9863 T=0.0137
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9968 T=0.0032
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=0.9851 T=0.0149
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=0.999 T=0.001
1000Genomes American Sub 694 C=1.000 T=0.000
KOREAN population from KRGDB KOREAN Study-wide 2918 C=0.9794 T=0.0206
Korean Genome Project KOREAN Study-wide 1832 C=0.9793 T=0.0207
A Vietnamese Genetic Variation Database Global Study-wide 614 C=0.987 T=0.013
SGDP_PRJ Global Study-wide 6 C=0.5 T=0.5
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.65170544C>G
GRCh38.p14 chr 12 NC_000012.12:g.65170544C>T
GRCh37.p13 chr 12 NC_000012.11:g.65564324C>G
GRCh37.p13 chr 12 NC_000012.11:g.65564324C>T
LEMD3 RefSeqGene NG_016210.2:g.5974C>G
LEMD3 RefSeqGene NG_016210.2:g.5974C>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.948C>G L [CTC] > L [CTG] Coding Sequence Variant
inner nuclear membrane protein Man1 isoform 1 NP_055134.2:p.Leu316= L (Leu) > L (Leu) Synonymous Variant
LEMD3 transcript variant 1 NM_014319.5:c.948C>T L [CTC] > L [CTT] Coding Sequence Variant
inner nuclear membrane protein Man1 isoform 1 NP_055134.2:p.Leu316= L (Leu) > L (Leu) Synonymous Variant
LEMD3 transcript variant 2 NM_001167614.2:c.948C>G L [CTC] > L [CTG] Coding Sequence Variant
inner nuclear membrane protein Man1 isoform 2 NP_001161086.1:p.Leu316= L (Leu) > L (Leu) Synonymous Variant
LEMD3 transcript variant 2 NM_001167614.2:c.948C>T L [CTC] > L [CTT] Coding Sequence Variant
inner nuclear membrane protein Man1 isoform 2 NP_001161086.1:p.Leu316= L (Leu) > L (Leu) 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: 318315 )
ClinVar Accession Disease Names Clinical Significance
RCV000291631.3 Dermatofibrosis lenticularis disseminata Benign
RCV000972081.4 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.65170544= NC_000012.12:g.65170544C>G NC_000012.12:g.65170544C>T
GRCh37.p13 chr 12 NC_000012.11:g.65564324= NC_000012.11:g.65564324C>G NC_000012.11:g.65564324C>T
LEMD3 RefSeqGene NG_016210.2:g.5974= NG_016210.2:g.5974C>G NG_016210.2:g.5974C>T
LEMD3 transcript variant 1 NM_014319.5:c.948= NM_014319.5:c.948C>G NM_014319.5:c.948C>T
LEMD3 transcript variant 1 NM_014319.4:c.948= NM_014319.4:c.948C>G NM_014319.4:c.948C>T
LEMD3 transcript variant 2 NM_001167614.2:c.948= NM_001167614.2:c.948C>G NM_001167614.2:c.948C>T
LEMD3 transcript variant 2 NM_001167614.1:c.948= NM_001167614.1:c.948C>G NM_001167614.1:c.948C>T
inner nuclear membrane protein Man1 isoform 1 NP_055134.2:p.Leu316= NP_055134.2:p.Leu316= NP_055134.2:p.Leu316=
inner nuclear membrane protein Man1 isoform 2 NP_001161086.1:p.Leu316= NP_001161086.1:p.Leu316= NP_001161086.1:p.Leu316=
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#.

32 SubSNP, 15 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss462924270 Sep 17, 2011 (135)
2 1000GENOMES ss491046651 May 04, 2012 (137)
3 NHLBI-ESP ss713103964 Apr 25, 2013 (138)
4 JMKIDD_LAB ss1067535686 Aug 21, 2014 (142)
5 1000GENOMES ss1345388676 Aug 21, 2014 (142)
6 EVA_EXAC ss1691001098 Apr 01, 2015 (144)
7 HUMAN_LONGEVITY ss2190549253 Dec 20, 2016 (150)
8 GRF ss2699937838 Nov 08, 2017 (151)
9 GNOMAD ss2739961010 Nov 08, 2017 (151)
10 GNOMAD ss2748909674 Nov 08, 2017 (151)
11 GNOMAD ss2911592383 Nov 08, 2017 (151)
12 EVA ss3750590932 Jul 13, 2019 (153)
13 KHV_HUMAN_GENOMES ss3815923188 Jul 13, 2019 (153)
14 EVA ss3824748473 Apr 27, 2020 (154)
15 SGDP_PRJ ss3878469078 Apr 27, 2020 (154)
16 KRGDB ss3927132011 Apr 27, 2020 (154)
17 KOGIC ss3972124004 Apr 27, 2020 (154)
18 EVA ss3986576529 Apr 26, 2021 (155)
19 TOPMED ss4921615606 Apr 26, 2021 (155)
20 TOPMED ss4921615607 Apr 26, 2021 (155)
21 TOMMO_GENOMICS ss5206754097 Apr 26, 2021 (155)
22 EVA ss5236907257 Apr 26, 2021 (155)
23 1000G_HIGH_COVERAGE ss5291139887 Oct 16, 2022 (156)
24 TRAN_CS_UWATERLOO ss5314436034 Oct 16, 2022 (156)
25 EVA ss5406232405 Oct 16, 2022 (156)
26 HUGCELL_USP ss5485851209 Oct 16, 2022 (156)
27 1000G_HIGH_COVERAGE ss5588793443 Oct 16, 2022 (156)
28 SANFORD_IMAGENETICS ss5653339108 Oct 16, 2022 (156)
29 TOMMO_GENOMICS ss5756675139 Oct 16, 2022 (156)
30 YY_MCH ss5813379758 Oct 16, 2022 (156)
31 EVA ss5904761907 Oct 16, 2022 (156)
32 EVA ss5944707228 Oct 16, 2022 (156)
33 1000Genomes NC_000012.11 - 65564324 Oct 12, 2018 (152)
34 1000Genomes_30x NC_000012.12 - 65170544 Oct 16, 2022 (156)
35 ExAC NC_000012.11 - 65564324 Oct 12, 2018 (152)
36 gnomAD - Genomes NC_000012.12 - 65170544 Apr 26, 2021 (155)
37 gnomAD - Exomes NC_000012.11 - 65564324 Jul 13, 2019 (153)
38 GO Exome Sequencing Project NC_000012.11 - 65564324 Oct 12, 2018 (152)
39 KOREAN population from KRGDB NC_000012.11 - 65564324 Apr 27, 2020 (154)
40 Korean Genome Project NC_000012.12 - 65170544 Apr 27, 2020 (154)
41 SGDP_PRJ NC_000012.11 - 65564324 Apr 27, 2020 (154)
42 8.3KJPN NC_000012.11 - 65564324 Apr 26, 2021 (155)
43 14KJPN NC_000012.12 - 65170544 Oct 16, 2022 (156)
44 TopMed

Submission ignored due to conflicting rows:
Row 137161263 (NC_000012.12:65170543:C:G 3/264690)
Row 137161264 (NC_000012.12:65170543:C:T 233/264690)

- Apr 26, 2021 (155)
45 TopMed

Submission ignored due to conflicting rows:
Row 137161263 (NC_000012.12:65170543:C:G 3/264690)
Row 137161264 (NC_000012.12:65170543:C:T 233/264690)

- Apr 26, 2021 (155)
46 A Vietnamese Genetic Variation Database NC_000012.11 - 65564324 Jul 13, 2019 (153)
47 ALFA NC_000012.12 - 65170544 Apr 26, 2021 (155)
48 ClinVar RCV000291631.3 Oct 16, 2022 (156)
49 ClinVar RCV000972081.4 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
12229630018, ss4921615606 NC_000012.12:65170543:C:G NC_000012.12:65170543:C:G (self)
58151406, 1305252, 9195738, 1205931, 34309405, 30486058, 64723404, 7165941, ss462924270, ss491046651, ss713103964, ss1067535686, ss1345388676, ss1691001098, ss2699937838, ss2739961010, ss2748909674, ss2911592383, ss3750590932, ss3824748473, ss3878469078, ss3927132011, ss3986576529, ss5206754097, ss5406232405, ss5653339108, ss5944707228 NC_000012.11:65564323:C:T NC_000012.12:65170543:C:T (self)
RCV000291631.3, RCV000972081.4, 76319378, 410105834, 28502005, 90512243, 12229630018, ss2190549253, ss3815923188, ss3972124004, ss4921615607, ss5236907257, ss5291139887, ss5314436034, ss5485851209, ss5588793443, ss5756675139, ss5813379758, ss5904761907 NC_000012.12:65170543:C:T NC_000012.12:65170543: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 rs183253527

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