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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.

rs115704555

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:1022188 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.016854 (4461/264690, TOPMED)
G=0.003964 (989/249478, GnomAD_exome)
G=0.016603 (2328/140214, GnomAD) (+ 8 more)
G=0.004934 (592/119976, ExAC)
G=0.00837 (199/23780, ALFA)
G=0.01761 (229/13004, GO-ESP)
G=0.0155 (99/6404, 1000G_30x)
G=0.0142 (71/5008, 1000G)
G=0.005 (1/216, Qatari)
A=0.5 (1/2, SGDP_PRJ)
G=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
AGRN : Intron Variant
Publications
1 citation
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 23780 A=0.99163 G=0.00837 0.983768 0.000505 0.015728 18
European Sub 15936 A=0.99956 G=0.00044 0.999121 0.0 0.000879 0
African Sub 3578 A=0.9508 G=0.0492 0.904975 0.003354 0.091671 0
African Others Sub 122 A=0.926 G=0.074 0.852459 0.0 0.147541 0
African American Sub 3456 A=0.9517 G=0.0483 0.906829 0.003472 0.089699 1
Asian Sub 172 A=1.000 G=0.000 1.0 0.0 0.0 N/A
East Asian Sub 114 A=1.000 G=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 58 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 154 A=0.994 G=0.006 0.987013 0.0 0.012987 0
Latin American 2 Sub 616 A=0.998 G=0.002 0.996753 0.0 0.003247 0
South Asian Sub 98 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Sub 3226 A=0.9957 G=0.0043 0.991321 0.0 0.008679 0


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 A=0.983146 G=0.016854
gnomAD - Exomes Global Study-wide 249478 A=0.996036 G=0.003964
gnomAD - Exomes European Sub 133552 A=0.999828 G=0.000172
gnomAD - Exomes Asian Sub 48984 A=0.99984 G=0.00016
gnomAD - Exomes American Sub 34580 A=0.99786 G=0.00214
gnomAD - Exomes African Sub 16210 A=0.94633 G=0.05367
gnomAD - Exomes Ashkenazi Jewish Sub 10042 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6110 A=0.9977 G=0.0023
gnomAD - Genomes Global Study-wide 140214 A=0.983397 G=0.016603
gnomAD - Genomes European Sub 75916 A=0.99980 G=0.00020
gnomAD - Genomes African Sub 42032 A=0.94685 G=0.05315
gnomAD - Genomes American Sub 13658 A=0.99649 G=0.00351
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3130 A=0.9997 G=0.0003
gnomAD - Genomes Other Sub 2154 A=0.9861 G=0.0139
ExAC Global Study-wide 119976 A=0.995066 G=0.004934
ExAC Europe Sub 72196 A=0.99985 G=0.00015
ExAC Asian Sub 25130 A=0.99980 G=0.00020
ExAC American Sub 11552 A=0.99836 G=0.00164
ExAC African Sub 10208 A=0.94553 G=0.05447
ExAC Other Sub 890 A=0.999 G=0.001
Allele Frequency Aggregator Total Global 23780 A=0.99163 G=0.00837
Allele Frequency Aggregator European Sub 15936 A=0.99956 G=0.00044
Allele Frequency Aggregator African Sub 3578 A=0.9508 G=0.0492
Allele Frequency Aggregator Other Sub 3226 A=0.9957 G=0.0043
Allele Frequency Aggregator Latin American 2 Sub 616 A=0.998 G=0.002
Allele Frequency Aggregator Asian Sub 172 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 154 A=0.994 G=0.006
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 13004 A=0.98239 G=0.01761
GO Exome Sequencing Project European American Sub 8598 A=0.9999 G=0.0001
GO Exome Sequencing Project African American Sub 4406 A=0.9483 G=0.0517
1000Genomes_30x Global Study-wide 6404 A=0.9845 G=0.0155
1000Genomes_30x African Sub 1786 A=0.9462 G=0.0538
1000Genomes_30x Europe Sub 1266 A=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.997 G=0.003
1000Genomes Global Study-wide 5008 A=0.9858 G=0.0142
1000Genomes African Sub 1322 A=0.9486 G=0.0514
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=1.0000 G=0.0000
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.996 G=0.004
Qatari Global Study-wide 216 A=0.995 G=0.005
SGDP_PRJ Global Study-wide 2 A=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 1 NC_000001.11:g.1022188A>G
GRCh37.p13 chr 1 NC_000001.10:g.957568A>G
AGRN RefSeqGene (LRG_198) NG_016346.1:g.7066A>G
LOC126805576 genomic region NG_081901.1:g.897A>G
Gene: AGRN, agrin (plus strand)
Molecule type Change Amino acid[Codon] SO Term
AGRN transcript variant 1 NM_001305275.2:c.202-13A>G N/A Intron Variant
AGRN transcript variant 2 NM_198576.4:c.202-13A>G N/A Intron Variant
AGRN transcript variant 3 NM_001364727.2:c. N/A Genic Upstream Transcript Variant
AGRN transcript variant X1 XM_005244749.4:c.202-13A>G N/A Intron Variant
AGRN transcript variant X2 XM_011541429.3:c.202-13A>G N/A Intron Variant
AGRN transcript variant X3 XM_047419836.1:c.202-13A>G N/A Intron Variant
AGRN transcript variant X4 XM_047419837.1:c. N/A Genic Upstream Transcript Variant
AGRN transcript variant X5 XM_047419838.1:c. N/A Genic 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: G (allele ID: 249265 )
ClinVar Accession Disease Names Clinical Significance
RCV000250556.2 not specified Benign
RCV002058480.3 Congenital myasthenic syndrome 8 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 A= G
GRCh38.p14 chr 1 NC_000001.11:g.1022188= NC_000001.11:g.1022188A>G
GRCh37.p13 chr 1 NC_000001.10:g.957568= NC_000001.10:g.957568A>G
AGRN RefSeqGene (LRG_198) NG_016346.1:g.7066= NG_016346.1:g.7066A>G
LOC126805576 genomic region NG_081901.1:g.897= NG_081901.1:g.897A>G
AGRN transcript variant 1 NM_001305275.2:c.202-13= NM_001305275.2:c.202-13A>G
AGRN transcript variant 2 NM_198576.3:c.202-13= NM_198576.3:c.202-13A>G
AGRN transcript variant 2 NM_198576.4:c.202-13= NM_198576.4:c.202-13A>G
AGRN transcript variant X1 XM_005244748.1:c.202-13= XM_005244748.1:c.202-13A>G
AGRN transcript variant X2 XM_005244749.1:c.202-13= XM_005244749.1:c.202-13A>G
AGRN transcript variant X1 XM_005244749.4:c.202-13= XM_005244749.4:c.202-13A>G
AGRN transcript variant X2 XM_011541429.3:c.202-13= XM_011541429.3:c.202-13A>G
AGRN transcript variant X3 XM_047419836.1:c.202-13= XM_047419836.1:c.202-13A>G
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#.

24 SubSNP, 10 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss218191426 Jul 14, 2010 (132)
2 1000GENOMES ss489714337 May 04, 2012 (137)
3 ILLUMINA ss534033406 Sep 08, 2015 (146)
4 NHLBI-ESP ss712260987 Apr 25, 2013 (138)
5 1000GENOMES ss1289346640 Aug 21, 2014 (142)
6 EVA_EXAC ss1685222275 Apr 01, 2015 (144)
7 WEILL_CORNELL_DGM ss1917962736 Feb 12, 2016 (147)
8 JJLAB ss2019499358 Sep 14, 2016 (149)
9 HUMAN_LONGEVITY ss2159378623 Dec 20, 2016 (150)
10 GNOMAD ss2730994321 Nov 08, 2017 (151)
11 GNOMAD ss2746172150 Nov 08, 2017 (151)
12 GNOMAD ss2750661044 Nov 08, 2017 (151)
13 ILLUMINA ss3626006914 Oct 11, 2018 (152)
14 EVA ss3823542322 Apr 25, 2020 (154)
15 SGDP_PRJ ss3848000980 Apr 25, 2020 (154)
16 EVA ss3986090948 Apr 25, 2021 (155)
17 TOPMED ss4436491551 Apr 25, 2021 (155)
18 1000G_HIGH_COVERAGE ss5240870207 Oct 12, 2022 (156)
19 EVA ss5316194760 Oct 12, 2022 (156)
20 HUGCELL_USP ss5442117547 Oct 12, 2022 (156)
21 1000G_HIGH_COVERAGE ss5512497618 Oct 12, 2022 (156)
22 SANFORD_IMAGENETICS ss5624753497 Oct 12, 2022 (156)
23 EVA ss5906711412 Oct 12, 2022 (156)
24 EVA ss5936585975 Oct 12, 2022 (156)
25 1000Genomes NC_000001.10 - 957568 Oct 11, 2018 (152)
26 1000Genomes_30x NC_000001.11 - 1022188 Oct 12, 2022 (156)
27 ExAC NC_000001.10 - 957568 Oct 11, 2018 (152)
28 gnomAD - Genomes NC_000001.11 - 1022188 Apr 25, 2021 (155)
29 gnomAD - Exomes NC_000001.10 - 957568 Jul 12, 2019 (153)
30 GO Exome Sequencing Project NC_000001.10 - 957568 Oct 11, 2018 (152)
31 Qatari NC_000001.10 - 957568 Apr 25, 2020 (154)
32 SGDP_PRJ NC_000001.10 - 957568 Apr 25, 2020 (154)
33 TopMed NC_000001.11 - 1022188 Apr 25, 2021 (155)
34 ALFA NC_000001.11 - 1022188 Apr 25, 2021 (155)
35 ClinVar RCV000250556.2 Oct 11, 2018 (152)
36 ClinVar RCV002058480.3 Oct 12, 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
11656, 4395729, 9129, 1059, 4666, 17960, ss218191426, ss489714337, ss534033406, ss712260987, ss1289346640, ss1685222275, ss1917962736, ss2019499358, ss2730994321, ss2746172150, ss2750661044, ss3626006914, ss3823542322, ss3848000980, ss3986090948, ss5316194760, ss5624753497, ss5936585975 NC_000001.10:957567:A:G NC_000001.11:1022187:A:G (self)
RCV000250556.2, RCV002058480.3, 23553, 115931, 97886, 3529031361, ss2159378623, ss4436491551, ss5240870207, ss5442117547, ss5512497618, ss5906711412 NC_000001.11:1022187:A:G NC_000001.11:1022187:A:G (self)
Help

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

1 citation for rs115704555
PMID Title Author Year Journal
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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.post825+45319f0