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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.

rs4614203

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:780616 (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 / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000971 (257/264690, TOPMED)
A=0.000648 (89/137428, GnomAD)
A=0.00064 (18/28256, 14KJPN) (+ 8 more)
A=0.00084 (14/16760, 8.3KJPN)
A=0.00046 (7/15150, ALFA)
A=0.0016 (10/6404, 1000G_30x)
A=0.0150 (44/2926, KOREAN)
A=0.002 (1/600, NorthernSweden)
A=0.000 (0/558, SGDP_PRJ)
A=0.005 (1/216, Qatari)
A=0.00 (0/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01409 : Intron Variant
LOC100288069 : 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 15150 A=0.00046 G=0.00000, T=0.99954
European Sub 11424 A=0.00044 G=0.00000, T=0.99956
African Sub 2294 A=0.0004 G=0.0000, T=0.9996
African Others Sub 84 A=0.00 G=0.00, T=1.00
African American Sub 2210 A=0.0005 G=0.0000, T=0.9995
Asian Sub 108 A=0.000 G=0.000, T=1.000
East Asian Sub 84 A=0.00 G=0.00, T=1.00
Other Asian Sub 24 A=0.00 G=0.00, T=1.00
Latin American 1 Sub 146 A=0.007 G=0.000, T=0.993
Latin American 2 Sub 610 A=0.000 G=0.000, T=1.000
South Asian Sub 94 A=0.00 G=0.00, T=1.00
Other Sub 474 A=0.000 G=0.000, T=1.000


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=0.000971 T=0.999029
gnomAD - Genomes Global Study-wide 137428 A=0.000648 T=0.999352
gnomAD - Genomes European Sub 74648 A=0.00017 T=0.99983
gnomAD - Genomes African Sub 40940 A=0.00042 T=0.99958
gnomAD - Genomes American Sub 13356 A=0.00404 T=0.99596
gnomAD - Genomes Ashkenazi Jewish Sub 3288 A=0.0000 T=1.0000
gnomAD - Genomes East Asian Sub 3094 A=0.0000 T=1.0000
gnomAD - Genomes Other Sub 2102 A=0.0024 T=0.9976
14KJPN JAPANESE Study-wide 28256 A=0.00064 T=0.99936
8.3KJPN JAPANESE Study-wide 16760 A=0.00084 T=0.99916
Allele Frequency Aggregator Total Global 15150 A=0.00046 G=0.00000, T=0.99954
Allele Frequency Aggregator European Sub 11424 A=0.00044 G=0.00000, T=0.99956
Allele Frequency Aggregator African Sub 2294 A=0.0004 G=0.0000, T=0.9996
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.000 G=0.000, T=1.000
Allele Frequency Aggregator Other Sub 474 A=0.000 G=0.000, T=1.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.007 G=0.000, T=0.993
Allele Frequency Aggregator Asian Sub 108 A=0.000 G=0.000, T=1.000
Allele Frequency Aggregator South Asian Sub 94 A=0.00 G=0.00, T=1.00
1000Genomes_30x Global Study-wide 6404 A=0.0016 T=0.9984
1000Genomes_30x African Sub 1786 A=0.0006 T=0.9994
1000Genomes_30x Europe Sub 1266 A=0.0008 T=0.9992
1000Genomes_30x South Asian Sub 1202 A=0.0000 T=1.0000
1000Genomes_30x East Asian Sub 1170 A=0.0009 T=0.9991
1000Genomes_30x American Sub 980 A=0.007 T=0.993
KOREAN population from KRGDB KOREAN Study-wide 2926 A=0.0150 T=0.9850
Northern Sweden ACPOP Study-wide 600 A=0.002 T=0.998
SGDP_PRJ Global Study-wide 558 A=0.000 T=1.000
Qatari Global Study-wide 216 A=0.005 T=0.995
The Danish reference pan genome Danish Study-wide 40 A=0.00 T=1.00
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.780616A>G
GRCh38.p14 chr 1 NC_000001.11:g.780616A>T
GRCh37.p13 chr 1 NC_000001.10:g.715996A>G
GRCh37.p13 chr 1 NC_000001.10:g.715996A>T
Gene: LOC100288069, uncharacterized LOC100288069 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC100288069 transcript NR_168328.1:n. N/A Upstream Transcript Variant
Gene: LINC01409, uncharacterized LINC01409 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01409 transcript variant X1 XR_007065319.1:n. N/A Intron Variant
LINC01409 transcript variant X2 XR_007065320.1:n. N/A Intron 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 A= G T
GRCh38.p14 chr 1 NC_000001.11:g.780616= NC_000001.11:g.780616A>G NC_000001.11:g.780616A>T
GRCh37.p13 chr 1 NC_000001.10:g.715996= NC_000001.10:g.715996A>G NC_000001.10:g.715996A>T
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, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss6256880 Feb 20, 2003 (111)
2 SSAHASNP ss35256100 May 24, 2005 (125)
3 HGSV ss82118603 Dec 15, 2007 (130)
4 HUMANGENOME_JCVI ss97913172 Feb 13, 2009 (144)
5 ENSEMBL ss138907742 Dec 01, 2009 (131)
6 GMI ss275680538 May 04, 2012 (144)
7 SSMP ss647515849 Apr 25, 2013 (144)
8 DDI ss1425684724 Apr 01, 2015 (144)
9 EVA_GENOME_DK ss1573851057 Apr 01, 2015 (144)
10 WEILL_CORNELL_DGM ss1917959723 Feb 12, 2016 (147)
11 SYSTEMSBIOZJU ss2624264725 Nov 08, 2017 (151)
12 GRF ss2697374018 Nov 08, 2017 (151)
13 GNOMAD ss2750632929 Nov 08, 2017 (151)
14 SWEGEN ss2986147709 Nov 08, 2017 (151)
15 CSHL ss3343272178 Nov 08, 2017 (151)
16 URBANLAB ss3646581099 Oct 11, 2018 (152)
17 ACPOP ss3726715979 Jul 12, 2019 (153)
18 PACBIO ss3783302025 Jul 12, 2019 (153)
19 PACBIO ss3788979908 Jul 12, 2019 (153)
20 PACBIO ss3793852445 Jul 12, 2019 (153)
21 EVA ss3841782312 Apr 25, 2020 (154)
22 SGDP_PRJ ss3847993810 Apr 25, 2020 (154)
23 KRGDB ss3892833257 Apr 25, 2020 (154)
24 TOPMED ss4436422118 Apr 25, 2021 (155)
25 TOMMO_GENOMICS ss5142049409 Apr 25, 2021 (155)
26 1000G_HIGH_COVERAGE ss5240861370 Oct 12, 2022 (156)
27 1000G_HIGH_COVERAGE ss5512485609 Oct 12, 2022 (156)
28 SANFORD_IMAGENETICS ss5624747865 Oct 12, 2022 (156)
29 TOMMO_GENOMICS ss5666187691 Oct 12, 2022 (156)
30 YY_MCH ss5800243122 Oct 12, 2022 (156)
31 EVA ss5831417611 Oct 12, 2022 (156)
32 EVA ss5979925970 Oct 12, 2022 (156)
33 1000Genomes_30x NC_000001.11 - 780616 Oct 12, 2022 (156)
34 The Danish reference pan genome NC_000001.10 - 715996 Apr 25, 2020 (154)
35 gnomAD - Genomes NC_000001.11 - 780616 Apr 25, 2021 (155)
36 KOREAN population from KRGDB NC_000001.10 - 715996 Apr 25, 2020 (154)
37 Northern Sweden NC_000001.10 - 715996 Jul 12, 2019 (153)
38 Qatari NC_000001.10 - 715996 Apr 25, 2020 (154)
39 SGDP_PRJ NC_000001.10 - 715996 Apr 25, 2020 (154)
40 8.3KJPN NC_000001.10 - 715996 Apr 25, 2021 (155)
41 14KJPN NC_000001.11 - 780616 Oct 12, 2022 (156)
42 TopMed NC_000001.11 - 780616 Apr 25, 2021 (155)
43 ALFA NC_000001.11 - 780616 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).

Associated ID History Updated (Build)
rs60400566 May 25, 2008 (130)
rs71507457 Jul 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
10225253219 NC_000001.11:780615:A:G NC_000001.11:780615:A:G (self)
ss35256100, ss82118603 NC_000001.8:755858:A:T NC_000001.11:780615:A:T (self)
ss275680538 NC_000001.9:705858:A:T NC_000001.11:780615:A:T (self)
1358291, 10651, 844, 1653, 10790, 18716, ss647515849, ss1425684724, ss1573851057, ss1917959723, ss2624264725, ss2697374018, ss2750632929, ss2986147709, ss3343272178, ss3726715979, ss3783302025, ss3788979908, ss3793852445, ss3847993810, ss3892833257, ss5142049409, ss5624747865, ss5831417611, ss5979925970 NC_000001.10:715995:A:T NC_000001.11:780615:A:T (self)
11544, 53579, 24795, 28453, 10225253219, ss3646581099, ss3841782312, ss4436422118, ss5240861370, ss5512485609, ss5666187691, ss5800243122 NC_000001.11:780615:A:T NC_000001.11:780615:A:T (self)
ss6256880, ss97913172, ss138907742 NT_004350.19:194627:A:T NC_000001.11:780615:A: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 rs4614203

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