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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.

rs199539318

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:53920646 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000336 (89/264690, TOPMED)
G=0.000397 (99/249414, GnomAD_exome)
G=0.000185 (26/140262, GnomAD) (+ 12 more)
G=0.000455 (55/120752, ExAC)
G=0.00024 (19/79484, ALFA)
G=0.00055 (43/78700, PAGE_STUDY)
G=0.00191 (54/28258, 14KJPN)
G=0.00197 (33/16760, 8.3KJPN)
G=0.0008 (5/6404, 1000G_30x)
G=0.0004 (2/5008, 1000G)
G=0.0044 (13/2922, KOREAN)
G=0.0033 (6/1832, Korea1K)
G=0.005 (4/792, PRJEB37584)
C=0.5 (1/2, SGDP_PRJ)
G=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LRRC1 : Missense 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 79484 C=0.99976 G=0.00024
European Sub 69394 C=1.00000 G=0.00000
African Sub 3698 C=1.0000 G=0.0000
African Others Sub 166 C=1.000 G=0.000
African American Sub 3532 C=1.0000 G=0.0000
Asian Sub 3274 C=0.9954 G=0.0046
East Asian Sub 2648 C=0.9951 G=0.0049
Other Asian Sub 626 C=0.997 G=0.003
Latin American 1 Sub 436 C=1.000 G=0.000
Latin American 2 Sub 928 C=1.000 G=0.000
South Asian Sub 274 C=1.000 G=0.000
Other Sub 1480 C=0.9973 G=0.0027


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=0.999664 G=0.000336
gnomAD - Exomes Global Study-wide 249414 C=0.999603 G=0.000397
gnomAD - Exomes European Sub 134700 C=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 48570 C=0.99813 G=0.00187
gnomAD - Exomes American Sub 34528 C=0.99988 G=0.00012
gnomAD - Exomes African Sub 15488 C=0.99987 G=0.00013
gnomAD - Exomes Ashkenazi Jewish Sub 10070 C=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6058 C=0.9997 G=0.0003
gnomAD - Genomes Global Study-wide 140262 C=0.999815 G=0.000185
gnomAD - Genomes European Sub 75956 C=1.00000 G=0.00000
gnomAD - Genomes African Sub 42038 C=0.99986 G=0.00014
gnomAD - Genomes American Sub 13658 C=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 C=0.9939 G=0.0061
gnomAD - Genomes Other Sub 2152 C=0.9995 G=0.0005
ExAC Global Study-wide 120752 C=0.999545 G=0.000455
ExAC Europe Sub 73344 C=1.00000 G=0.00000
ExAC Asian Sub 25128 C=0.99789 G=0.00211
ExAC American Sub 11572 C=0.99983 G=0.00017
ExAC African Sub 9808 C=1.0000 G=0.0000
ExAC Other Sub 900 C=1.000 G=0.000
Allele Frequency Aggregator Total Global 79484 C=0.99976 G=0.00024
Allele Frequency Aggregator European Sub 69394 C=1.00000 G=0.00000
Allele Frequency Aggregator African Sub 3698 C=1.0000 G=0.0000
Allele Frequency Aggregator Asian Sub 3274 C=0.9954 G=0.0046
Allele Frequency Aggregator Other Sub 1480 C=0.9973 G=0.0027
Allele Frequency Aggregator Latin American 2 Sub 928 C=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 436 C=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 274 C=1.000 G=0.000
The PAGE Study Global Study-wide 78700 C=0.99945 G=0.00055
The PAGE Study AfricanAmerican Sub 32516 C=0.99991 G=0.00009
The PAGE Study Mexican Sub 10810 C=1.00000 G=0.00000
The PAGE Study Asian Sub 8316 C=0.9964 G=0.0036
The PAGE Study PuertoRican Sub 7918 C=1.0000 G=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=0.9978 G=0.0022
The PAGE Study Cuban Sub 4230 C=1.0000 G=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 G=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 G=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 G=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 G=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 G=0.000
14KJPN JAPANESE Study-wide 28258 C=0.99809 G=0.00191
8.3KJPN JAPANESE Study-wide 16760 C=0.99803 G=0.00197
1000Genomes_30x Global Study-wide 6404 C=0.9992 G=0.0008
1000Genomes_30x African Sub 1786 C=1.0000 G=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 C=0.9957 G=0.0043
1000Genomes_30x American Sub 980 C=1.000 G=0.000
1000Genomes Global Study-wide 5008 C=0.9996 G=0.0004
1000Genomes African Sub 1322 C=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 C=0.9980 G=0.0020
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=1.000 G=0.000
1000Genomes American Sub 694 C=1.000 G=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9956 G=0.0044
Korean Genome Project KOREAN Study-wide 1832 C=0.9967 G=0.0033
CNV burdens in cranial meningiomas Global Study-wide 792 C=0.995 G=0.005
CNV burdens in cranial meningiomas CRM Sub 792 C=0.995 G=0.005
SGDP_PRJ Global Study-wide 2 C=0.5 G=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 6 NC_000006.12:g.53920646C>G
GRCh37.p13 chr 6 NC_000006.11:g.53785444C>G
Gene: LRRC1, leucine rich repeat containing 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LRRC1 transcript NM_018214.5:c.1301C>G A [GCA] > G [GGA] Coding Sequence Variant
leucine-rich repeat-containing protein 1 NP_060684.4:p.Ala434Gly A (Ala) > G (Gly) Missense Variant
LRRC1 transcript variant X3 XM_017010997.2:c. N/A Genic Downstream Transcript Variant
LRRC1 transcript variant X1 XM_011514727.3:c.1124C>G A [GCA] > G [GGA] Coding Sequence Variant
leucine-rich repeat-containing protein 1 isoform X1 XP_011513029.1:p.Ala375Gly A (Ala) > G (Gly) Missense Variant
LRRC1 transcript variant X4 XR_001743505.2:n. N/A Genic Downstream Transcript Variant
LRRC1 transcript variant X2 XR_007059279.1:n. N/A Genic Downstream 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= G
GRCh38.p14 chr 6 NC_000006.12:g.53920646= NC_000006.12:g.53920646C>G
GRCh37.p13 chr 6 NC_000006.11:g.53785444= NC_000006.11:g.53785444C>G
LRRC1 transcript NM_018214.5:c.1301= NM_018214.5:c.1301C>G
LRRC1 transcript NM_018214.4:c.1301= NM_018214.4:c.1301C>G
LRRC1 transcript variant X1 XM_011514727.3:c.1124= XM_011514727.3:c.1124C>G
LRRC1 transcript variant X2 XM_011514727.2:c.1124= XM_011514727.2:c.1124C>G
LRRC1 transcript variant X2 XM_011514727.1:c.1124= XM_011514727.1:c.1124C>G
leucine-rich repeat-containing protein 1 NP_060684.4:p.Ala434= NP_060684.4:p.Ala434Gly
leucine-rich repeat-containing protein 1 isoform X1 XP_011513029.1:p.Ala375= XP_011513029.1:p.Ala375Gly
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#.

44 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 EXOME_CHIP ss491387565 May 04, 2012 (137)
2 SSMP ss653160560 Apr 25, 2013 (138)
3 ILLUMINA ss780850658 Aug 21, 2014 (142)
4 ILLUMINA ss783534505 Aug 21, 2014 (142)
5 1000GENOMES ss1320211611 Aug 21, 2014 (142)
6 EVA_EXAC ss1688368283 Apr 01, 2015 (144)
7 ILLUMINA ss1752642062 Sep 08, 2015 (146)
8 ILLUMINA ss1917806968 Feb 12, 2016 (147)
9 ILLUMINA ss1946180838 Feb 12, 2016 (147)
10 ILLUMINA ss1958912433 Feb 12, 2016 (147)
11 HUMAN_LONGEVITY ss2284251121 Dec 20, 2016 (150)
12 GNOMAD ss2735861287 Nov 08, 2017 (151)
13 GNOMAD ss2747645350 Nov 08, 2017 (151)
14 GNOMAD ss2839222615 Nov 08, 2017 (151)
15 AFFY ss2985370867 Nov 08, 2017 (151)
16 ILLUMINA ss3022624111 Nov 08, 2017 (151)
17 ILLUMINA ss3629554134 Oct 12, 2018 (152)
18 ILLUMINA ss3635069578 Oct 12, 2018 (152)
19 ILLUMINA ss3640776878 Oct 12, 2018 (152)
20 ILLUMINA ss3644913884 Oct 12, 2018 (152)
21 ILLUMINA ss3653141126 Oct 12, 2018 (152)
22 ILLUMINA ss3654136404 Oct 12, 2018 (152)
23 ILLUMINA ss3726349833 Jul 13, 2019 (153)
24 ILLUMINA ss3744555797 Jul 13, 2019 (153)
25 ILLUMINA ss3745369528 Jul 13, 2019 (153)
26 EVA ss3765046080 Jul 13, 2019 (153)
27 PAGE_CC ss3771296096 Jul 13, 2019 (153)
28 ILLUMINA ss3772863051 Jul 13, 2019 (153)
29 SGDP_PRJ ss3864621446 Apr 26, 2020 (154)
30 KRGDB ss3911439635 Apr 26, 2020 (154)
31 KOGIC ss3959070325 Apr 26, 2020 (154)
32 EVA ss3984569764 Apr 26, 2021 (155)
33 TOPMED ss4703687331 Apr 26, 2021 (155)
34 TOMMO_GENOMICS ss5177588499 Apr 26, 2021 (155)
35 EVA ss5237025539 Apr 26, 2021 (155)
36 1000G_HIGH_COVERAGE ss5268516257 Oct 13, 2022 (156)
37 EVA ss5315158462 Oct 13, 2022 (156)
38 EVA ss5365752405 Oct 13, 2022 (156)
39 1000G_HIGH_COVERAGE ss5554452774 Oct 13, 2022 (156)
40 TOMMO_GENOMICS ss5715662347 Oct 13, 2022 (156)
41 YY_MCH ss5807483981 Oct 13, 2022 (156)
42 EVA ss5848099332 Oct 13, 2022 (156)
43 EVA ss5883900223 Oct 13, 2022 (156)
44 EVA ss5968943043 Oct 13, 2022 (156)
45 1000Genomes NC_000006.11 - 53785444 Oct 12, 2018 (152)
46 1000Genomes_30x NC_000006.12 - 53920646 Oct 13, 2022 (156)
47 ExAC NC_000006.11 - 53785444 Oct 12, 2018 (152)
48 gnomAD - Genomes NC_000006.12 - 53920646 Apr 26, 2021 (155)
49 gnomAD - Exomes NC_000006.11 - 53785444 Jul 13, 2019 (153)
50 KOREAN population from KRGDB NC_000006.11 - 53785444 Apr 26, 2020 (154)
51 Korean Genome Project NC_000006.12 - 53920646 Apr 26, 2020 (154)
52 The PAGE Study NC_000006.12 - 53920646 Jul 13, 2019 (153)
53 CNV burdens in cranial meningiomas NC_000006.11 - 53785444 Apr 26, 2021 (155)
54 SGDP_PRJ NC_000006.11 - 53785444 Apr 26, 2020 (154)
55 8.3KJPN NC_000006.11 - 53785444 Apr 26, 2021 (155)
56 14KJPN NC_000006.12 - 53920646 Oct 13, 2022 (156)
57 TopMed NC_000006.12 - 53920646 Apr 26, 2021 (155)
58 ALFA NC_000006.12 - 53920646 Apr 26, 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
32002966, 8404084, 5008060, 18617029, 119173, 16638426, 35557806, ss491387565, ss653160560, ss780850658, ss783534505, ss1320211611, ss1688368283, ss1752642062, ss1917806968, ss1946180838, ss1958912433, ss2735861287, ss2747645350, ss2839222615, ss2985370867, ss3022624111, ss3629554134, ss3635069578, ss3640776878, ss3644913884, ss3653141126, ss3654136404, ss3744555797, ss3745369528, ss3765046080, ss3772863051, ss3864621446, ss3911439635, ss3984569764, ss5177588499, ss5315158462, ss5365752405, ss5848099332, ss5968943043 NC_000006.11:53785443:C:G NC_000006.12:53920645:C:G (self)
41978709, 225791151, 15448326, 517565, 49499451, 541064889, 10734906919, ss2284251121, ss3726349833, ss3771296096, ss3959070325, ss4703687331, ss5237025539, ss5268516257, ss5554452774, ss5715662347, ss5807483981, ss5883900223 NC_000006.12:53920645:C:G NC_000006.12:53920645:C: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 rs199539318

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