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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr3:198038605 (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.

Variation Type
SNV Single Nucleotide Variation
C=0.000015 (4/264690, TOPMED)
C=0.000024 (6/251472, GnomAD_exome)
C=0.000014 (2/140308, GnomAD) (+ 3 more)
C=0.000033 (4/121410, ExAC)
C=0.00003 (1/35432, ALFA)
C=0.00015 (2/13006, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LMLN : Missense Variant
LMLN-AS1 : Non Coding Transcript Variant
0 citations
Genomic View
See rs on genome

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 3 NC_000003.12:g.198038605T>C
GRCh37.p13 chr 3 NC_000003.11:g.197765476T>C
LMLN RefSeqGene NG_047207.1:g.83406T>C
Gene: LMLN, leishmanolysin like peptidase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LMLN transcript variant 2 NM_033029.3:c.1906T>C W [TGG] > R [CGG] Coding Sequence Variant
leishmanolysin-like peptidase isoform 2 NP_149018.2:p.Trp636Arg W (Trp) > R (Arg) Missense Variant
LMLN transcript variant 1 NM_001136049.2:c.2017T>C W [TGG] > R [CGG] Coding Sequence Variant
leishmanolysin-like peptidase isoform 1 NP_001129521.2:p.Trp673Arg W (Trp) > R (Arg) Missense Variant
LMLN transcript variant 4 NR_026787.2:n.1790T>C N/A Non Coding Transcript Variant
LMLN transcript variant 3 NR_026786.2:n.1901T>C N/A Non Coding Transcript Variant
Gene: LMLN-AS1, LMLN antisense RNA 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LMLN-AS1 transcript NR_046669.1:n.267A>G N/A Non Coding Transcript Variant

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 35432 T=0.99997 C=0.00003
European Sub 26588 T=0.99996 C=0.00004
African Sub 2918 T=1.0000 C=0.0000
African Others Sub 114 T=1.000 C=0.000
African American Sub 2804 T=1.0000 C=0.0000
Asian Sub 112 T=1.000 C=0.000
East Asian Sub 86 T=1.00 C=0.00
Other Asian Sub 26 T=1.00 C=0.00
Latin American 1 Sub 500 T=1.000 C=0.000
Latin American 2 Sub 628 T=1.000 C=0.000
South Asian Sub 98 T=1.00 C=0.00
Other Sub 4588 T=1.0000 C=0.0000


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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 T=0.999985 C=0.000015
gnomAD - Exomes Global Study-wide 251472 T=0.999976 C=0.000024
gnomAD - Exomes European Sub 135396 T=0.999956 C=0.000044
gnomAD - Exomes Asian Sub 49010 T=1.00000 C=0.00000
gnomAD - Exomes American Sub 34592 T=1.00000 C=0.00000
gnomAD - Exomes African Sub 16256 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6138 T=1.0000 C=0.0000
gnomAD - Genomes Global Study-wide 140308 T=0.999986 C=0.000014
gnomAD - Genomes European Sub 75966 T=0.99997 C=0.00003
gnomAD - Genomes African Sub 42068 T=1.00000 C=0.00000
gnomAD - Genomes American Sub 13666 T=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3134 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2152 T=1.0000 C=0.0000
ExAC Global Study-wide 121410 T=0.999967 C=0.000033
ExAC Europe Sub 73352 T=0.99995 C=0.00005
ExAC Asian Sub 25166 T=1.00000 C=0.00000
ExAC American Sub 11578 T=1.00000 C=0.00000
ExAC African Sub 10406 T=1.00000 C=0.00000
ExAC Other Sub 908 T=1.000 C=0.000
GO Exome Sequencing Project Global Study-wide 13006 T=0.99985 C=0.00015
GO Exome Sequencing Project European American Sub 8600 T=0.9998 C=0.0002
GO Exome Sequencing Project African American Sub 4406 T=1.0000 C=0.0000

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 T= C
GRCh38.p13 chr 3 NC_000003.12:g.198038605= NC_000003.12:g.198038605T>C
GRCh37.p13 chr 3 NC_000003.11:g.197765476= NC_000003.11:g.197765476T>C
LMLN RefSeqGene NG_047207.1:g.83406= NG_047207.1:g.83406T>C
LMLN transcript variant 2 NM_033029.3:c.1906= NM_033029.3:c.1906T>C
LMLN transcript variant 1 NM_001136049.2:c.2017= NM_001136049.2:c.2017T>C
LMLN transcript variant 3 NR_026786.2:n.1901= NR_026786.2:n.1901T>C
LMLN transcript variant 3 NR_026786.1:n.1918= NR_026786.1:n.1918T>C
LMLN transcript variant 4 NR_026787.2:n.1790= NR_026787.2:n.1790T>C
LMLN transcript variant 4 NR_026787.1:n.1807= NR_026787.1:n.1807T>C
LMLN-AS1 transcript NR_046669.1:n.267= NR_046669.1:n.267A>G
leishmanolysin-like peptidase isoform 2 NP_149018.2:p.Trp636= NP_149018.2:p.Trp636Arg
leishmanolysin-like peptidase isoform 1 NP_001129521.2:p.Trp673= NP_001129521.2:p.Trp673Arg

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#.

8 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712575321 Apr 25, 2013 (138)
2 EVA_EXAC ss1687370772 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2259715347 Dec 20, 2016 (150)
4 GNOMAD ss2734318179 Nov 08, 2017 (151)
5 TOPMED ss3417811440 Nov 08, 2017 (151)
6 EVA ss3823990034 Apr 25, 2020 (154)
7 GNOMAD ss4088965870 Apr 26, 2021 (155)
8 TOPMED ss4599698660 Apr 26, 2021 (155)
9 ExAC NC_000003.11 - 197765476 Oct 12, 2018 (152)
10 gnomAD - Genomes NC_000003.12 - 198038605 Apr 26, 2021 (155)
11 gnomAD - Exomes NC_000003.11 - 197765476 Jul 13, 2019 (153)
12 GO Exome Sequencing Project NC_000003.11 - 197765476 Oct 12, 2018 (152)
13 TopMed NC_000003.12 - 198038605 Apr 26, 2021 (155)
14 ALFA NC_000003.12 - 198038605 Apr 26, 2021 (155)

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
7325253, 3417278, 448296, ss712575321, ss1687370772, ss2734318179, ss3823990034 NC_000003.11:197765475:T:C NC_000003.12:198038604:T:C (self)
137472102, 273224511, 437076215, 4872000105, ss2259715347, ss3417811440, ss4088965870, ss4599698660 NC_000003.12:198038604:T:C NC_000003.12:198038604:T:C (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs369383533


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