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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.

rs1468844419

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:202310257 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/251456, GnomAD_exome)
T=0.00003 (1/32060, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LGR6 : Synonymous 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 32060 C=0.99997 T=0.00003 0.999938 0.0 6.2e-05 0
European Sub 23860 C=0.99996 T=0.00004 0.999916 0.0 0.000084 0
African Sub 2314 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 C=1.00 T=0.00 1.0 0.0 0.0 N/A
African American Sub 2230 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 C=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 498 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 628 C=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 4558 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A


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 251456 C=0.999996 T=0.000004
gnomAD - Exomes European Sub 135388 C=0.999993 T=0.000007
gnomAD - Exomes Asian Sub 49010 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34584 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16256 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6138 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 32060 C=0.99997 T=0.00003
Allele Frequency Aggregator European Sub 23860 C=0.99996 T=0.00004
Allele Frequency Aggregator Other Sub 4558 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2314 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 498 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 T=0.00
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 1 NC_000001.11:g.202310257C>T
GRCh37.p13 chr 1 NC_000001.10:g.202279385C>T
Gene: LGR6, leucine rich repeat containing G protein-coupled receptor 6 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LGR6 transcript variant 2 NM_021636.3:c.1311C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform 2 NP_067649.2:p.Phe437= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant 1 NM_001017403.2:c.1467C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform 1 precursor NP_001017403.1:p.Phe489= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant 3 NM_001017404.2:c.1050C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform 3 NP_001017404.1:p.Phe350= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X1 XM_005245404.4:c.1338C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X1 XP_005245461.1:p.Phe446= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X2 XM_011509838.3:c.1266C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X2 XP_011508140.1:p.Phe422= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X3 XM_011509839.3:c.1266C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X3 XP_011508141.1:p.Phe422= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X4 XM_047426928.1:c.1395C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X4 XP_047282884.1:p.Phe465= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X5 XM_017001996.2:c.1194C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X5 XP_016857485.1:p.Phe398= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X6 XM_047426929.1:c.1323C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X6 XP_047282885.1:p.Phe441= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X7 XM_011509840.3:c.1122C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X7 XP_011508142.1:p.Phe374= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X8 XM_047426930.1:c.1122C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X8 XP_047282886.1:p.Phe374= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X9 XM_047426931.1:c.1251C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X9 XP_047282887.1:p.Phe417= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X10 XM_047426932.1:c.978C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X10 XP_047282888.1:p.Phe326= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X11 XM_017001997.2:c.1065C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X11 XP_016857486.1:p.Phe355= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X12 XM_011509841.3:c.1065C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X12 XP_011508143.1:p.Phe355= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X13 XM_011509843.3:c.897C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X13 XP_011508145.1:p.Phe299= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X14 XM_011509842.3:c.897C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X13 XP_011508144.1:p.Phe299= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X15 XM_011509844.3:c.690C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X14 XP_011508146.1:p.Phe230= F (Phe) > F (Phe) Synonymous Variant
LGR6 transcript variant X16 XM_011509846.3:c.897C>T F [TTC] > F [TTT] Coding Sequence Variant
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X13 XP_011508148.1:p.Phe299= F (Phe) > F (Phe) Synonymous 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= T
GRCh38.p14 chr 1 NC_000001.11:g.202310257= NC_000001.11:g.202310257C>T
GRCh37.p13 chr 1 NC_000001.10:g.202279385= NC_000001.10:g.202279385C>T
LGR6 transcript variant X1 XM_005245404.4:c.1338= XM_005245404.4:c.1338C>T
LGR6 transcript variant X1 XM_005245404.3:c.1338= XM_005245404.3:c.1338C>T
LGR6 transcript variant X1 XM_005245404.2:c.1338= XM_005245404.2:c.1338C>T
LGR6 transcript variant X1 XM_005245404.1:c.1338= XM_005245404.1:c.1338C>T
LGR6 transcript variant X14 XM_011509842.3:c.897= XM_011509842.3:c.897C>T
LGR6 transcript variant X8 XM_011509842.2:c.897= XM_011509842.2:c.897C>T
LGR6 transcript variant X6 XM_011509842.1:c.897= XM_011509842.1:c.897C>T
LGR6 transcript variant X12 XM_011509841.3:c.1065= XM_011509841.3:c.1065C>T
LGR6 transcript variant X7 XM_011509841.2:c.1065= XM_011509841.2:c.1065C>T
LGR6 transcript variant X5 XM_011509841.1:c.1065= XM_011509841.1:c.1065C>T
LGR6 transcript variant 2 NM_021636.3:c.1311= NM_021636.3:c.1311C>T
LGR6 transcript variant 2 NM_021636.2:c.1311= NM_021636.2:c.1311C>T
LGR6 transcript variant X3 XM_011509839.3:c.1266= XM_011509839.3:c.1266C>T
LGR6 transcript variant X3 XM_011509839.2:c.1266= XM_011509839.2:c.1266C>T
LGR6 transcript variant X3 XM_011509839.1:c.1266= XM_011509839.1:c.1266C>T
LGR6 transcript variant X2 XM_011509838.3:c.1266= XM_011509838.3:c.1266C>T
LGR6 transcript variant X2 XM_011509838.2:c.1266= XM_011509838.2:c.1266C>T
LGR6 transcript variant X2 XM_011509838.1:c.1266= XM_011509838.1:c.1266C>T
LGR6 transcript variant X13 XM_011509843.3:c.897= XM_011509843.3:c.897C>T
LGR6 transcript variant X9 XM_011509843.2:c.897= XM_011509843.2:c.897C>T
LGR6 transcript variant X7 XM_011509843.1:c.897= XM_011509843.1:c.897C>T
LGR6 transcript variant X7 XM_011509840.3:c.1122= XM_011509840.3:c.1122C>T
LGR6 transcript variant X5 XM_011509840.2:c.1122= XM_011509840.2:c.1122C>T
LGR6 transcript variant X4 XM_011509840.1:c.1122= XM_011509840.1:c.1122C>T
LGR6 transcript variant X16 XM_011509846.3:c.897= XM_011509846.3:c.897C>T
LGR6 transcript variant X11 XM_011509846.2:c.897= XM_011509846.2:c.897C>T
LGR6 transcript variant X10 XM_011509846.1:c.897= XM_011509846.1:c.897C>T
LGR6 transcript variant X15 XM_011509844.3:c.690= XM_011509844.3:c.690C>T
LGR6 transcript variant X10 XM_011509844.2:c.690= XM_011509844.2:c.690C>T
LGR6 transcript variant X8 XM_011509844.1:c.690= XM_011509844.1:c.690C>T
LGR6 transcript variant 1 NM_001017403.2:c.1467= NM_001017403.2:c.1467C>T
LGR6 transcript variant 1 NM_001017403.1:c.1467= NM_001017403.1:c.1467C>T
LGR6 transcript variant X5 XM_017001996.2:c.1194= XM_017001996.2:c.1194C>T
LGR6 transcript variant X4 XM_017001996.1:c.1194= XM_017001996.1:c.1194C>T
LGR6 transcript variant X11 XM_017001997.2:c.1065= XM_017001997.2:c.1065C>T
LGR6 transcript variant X6 XM_017001997.1:c.1065= XM_017001997.1:c.1065C>T
LGR6 transcript variant 3 NM_001017404.2:c.1050= NM_001017404.2:c.1050C>T
LGR6 transcript variant 3 NM_001017404.1:c.1050= NM_001017404.1:c.1050C>T
LGR6 transcript variant X4 XM_047426928.1:c.1395= XM_047426928.1:c.1395C>T
LGR6 transcript variant X6 XM_047426929.1:c.1323= XM_047426929.1:c.1323C>T
LGR6 transcript variant X9 XM_047426931.1:c.1251= XM_047426931.1:c.1251C>T
LGR6 transcript variant X8 XM_047426930.1:c.1122= XM_047426930.1:c.1122C>T
LGR6 transcript variant X10 XM_047426932.1:c.978= XM_047426932.1:c.978C>T
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X1 XP_005245461.1:p.Phe446= XP_005245461.1:p.Phe446=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X13 XP_011508144.1:p.Phe299= XP_011508144.1:p.Phe299=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X12 XP_011508143.1:p.Phe355= XP_011508143.1:p.Phe355=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform 2 NP_067649.2:p.Phe437= NP_067649.2:p.Phe437=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X3 XP_011508141.1:p.Phe422= XP_011508141.1:p.Phe422=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X2 XP_011508140.1:p.Phe422= XP_011508140.1:p.Phe422=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X13 XP_011508145.1:p.Phe299= XP_011508145.1:p.Phe299=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X7 XP_011508142.1:p.Phe374= XP_011508142.1:p.Phe374=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X13 XP_011508148.1:p.Phe299= XP_011508148.1:p.Phe299=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X14 XP_011508146.1:p.Phe230= XP_011508146.1:p.Phe230=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform 1 precursor NP_001017403.1:p.Phe489= NP_001017403.1:p.Phe489=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X5 XP_016857485.1:p.Phe398= XP_016857485.1:p.Phe398=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X11 XP_016857486.1:p.Phe355= XP_016857486.1:p.Phe355=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform 3 NP_001017404.1:p.Phe350= NP_001017404.1:p.Phe350=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X4 XP_047282884.1:p.Phe465= XP_047282884.1:p.Phe465=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X6 XP_047282885.1:p.Phe441= XP_047282885.1:p.Phe441=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X9 XP_047282887.1:p.Phe417= XP_047282887.1:p.Phe417=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X8 XP_047282886.1:p.Phe374= XP_047282886.1:p.Phe374=
leucine-rich repeat-containing G-protein coupled receptor 6 isoform X10 XP_047282888.1:p.Phe326= XP_047282888.1:p.Phe326=
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#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2732186554 Nov 08, 2017 (151)
2 gnomAD - Exomes NC_000001.10 - 202279385 Jul 12, 2019 (153)
3 ALFA NC_000001.11 - 202310257 Apr 25, 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
1219548, ss2732186554 NC_000001.10:202279384:C:T NC_000001.11:202310256:C:T (self)
14641094556 NC_000001.11:202310256:C:T NC_000001.11:202310256: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 rs1468844419

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.post820+afb47a3d