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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.

rs145097404

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:109574002 (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=0.000083 (22/264690, TOPMED)
T=0.000216 (54/249802, GnomAD_exome)
T=0.000145 (28/192884, ALFA) (+ 10 more)
T=0.000093 (13/140214, GnomAD)
T=0.000240 (29/120726, ExAC)
T=0.00050 (39/78702, PAGE_STUDY)
T=0.00418 (118/28256, 14KJPN)
T=0.00400 (67/16760, 8.3KJPN)
T=0.00023 (3/13006, GO-ESP)
T=0.0006 (4/6404, 1000G_30x)
T=0.0008 (4/5008, 1000G)
T=0.0072 (21/2930, KOREAN)
T=0.0027 (5/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GNAI3 : 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 209294 C=0.999861 T=0.000139
European Sub 173942 C=0.999914 T=0.000086
African Sub 9790 C=1.0000 T=0.0000
African Others Sub 360 C=1.000 T=0.000
African American Sub 9430 C=1.0000 T=0.0000
Asian Sub 6348 C=0.9983 T=0.0017
East Asian Sub 4500 C=0.9976 T=0.0024
Other Asian Sub 1848 C=1.0000 T=0.0000
Latin American 1 Sub 796 C=1.000 T=0.000
Latin American 2 Sub 968 C=1.000 T=0.000
South Asian Sub 280 C=1.000 T=0.000
Other Sub 17170 C=0.99983 T=0.00017


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=0.999917 T=0.000083
gnomAD - Exomes Global Study-wide 249802 C=0.999784 T=0.000216
gnomAD - Exomes European Sub 134354 C=0.999866 T=0.000134
gnomAD - Exomes Asian Sub 48760 C=0.99947 T=0.00053
gnomAD - Exomes American Sub 34334 C=0.99983 T=0.00017
gnomAD - Exomes African Sub 16240 C=0.99982 T=0.00018
gnomAD - Exomes Ashkenazi Jewish Sub 10022 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6092 C=0.9998 T=0.0002
Allele Frequency Aggregator Total Global 192884 C=0.999855 T=0.000145
Allele Frequency Aggregator European Sub 163802 C=0.999915 T=0.000085
Allele Frequency Aggregator Other Sub 15736 C=0.99981 T=0.00019
Allele Frequency Aggregator Asian Sub 6348 C=0.9983 T=0.0017
Allele Frequency Aggregator African Sub 4954 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 968 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 796 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 280 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 140214 C=0.999907 T=0.000093
gnomAD - Genomes European Sub 75926 C=0.99988 T=0.00012
gnomAD - Genomes African Sub 42026 C=0.99998 T=0.00002
gnomAD - Genomes American Sub 13654 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=0.9990 T=0.0010
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
ExAC Global Study-wide 120726 C=0.999760 T=0.000240
ExAC Europe Sub 72988 C=0.99985 T=0.00015
ExAC Asian Sub 25010 C=0.99932 T=0.00068
ExAC American Sub 11502 C=0.99991 T=0.00009
ExAC African Sub 10324 C=1.00000 T=0.00000
ExAC Other Sub 902 C=1.000 T=0.000
The PAGE Study Global Study-wide 78702 C=0.99950 T=0.00050
The PAGE Study AfricanAmerican Sub 32516 C=0.99978 T=0.00022
The PAGE Study Mexican Sub 10810 C=0.99981 T=0.00019
The PAGE Study Asian Sub 8318 C=0.9969 T=0.0031
The PAGE Study PuertoRican Sub 7918 C=0.9999 T=0.0001
The PAGE Study NativeHawaiian Sub 4534 C=0.9996 T=0.0004
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=0.9997 T=0.0003
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
14KJPN JAPANESE Study-wide 28256 C=0.99582 T=0.00418
8.3KJPN JAPANESE Study-wide 16760 C=0.99600 T=0.00400
GO Exome Sequencing Project Global Study-wide 13006 C=0.99977 T=0.00023
GO Exome Sequencing Project European American Sub 8600 C=0.9998 T=0.0002
GO Exome Sequencing Project African American Sub 4406 C=0.9998 T=0.0002
1000Genomes_30x Global Study-wide 6404 C=0.9994 T=0.0006
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=0.9966 T=0.0034
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9992 T=0.0008
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=0.9960 T=0.0040
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.9928 T=0.0072
Korean Genome Project KOREAN Study-wide 1832 C=0.9973 T=0.0027
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.109574002C>T
GRCh37.p13 chr 1 NC_000001.10:g.110116624C>T
GNAI3 RefSeqGene NG_032795.1:g.30439C>T
Gene: GNAI3, G protein subunit alpha i3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GNAI3 transcript NM_006496.4:c.268C>T R [CGG] > W [TGG] Coding Sequence Variant
guanine nucleotide-binding protein G(i) subunit alpha-3 NP_006487.1:p.Arg90Trp R (Arg) > W (Trp) Missense 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.109574002= NC_000001.11:g.109574002C>T
GRCh37.p13 chr 1 NC_000001.10:g.110116624= NC_000001.10:g.110116624C>T
GNAI3 RefSeqGene NG_032795.1:g.30439= NG_032795.1:g.30439C>T
GNAI3 transcript NM_006496.4:c.268= NM_006496.4:c.268C>T
GNAI3 transcript NM_006496.3:c.268= NM_006496.3:c.268C>T
guanine nucleotide-binding protein G(i) subunit alpha-3 NP_006487.1:p.Arg90= NP_006487.1:p.Arg90Trp
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, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss328849815 May 09, 2011 (134)
2 NHLBI-ESP ss341980048 May 09, 2011 (134)
3 1000GENOMES ss489756254 May 04, 2012 (137)
4 EXOME_CHIP ss491297935 May 04, 2012 (137)
5 ILLUMINA ss534952514 Sep 08, 2015 (146)
6 ILLUMINA ss783571185 Sep 08, 2015 (146)
7 1000GENOMES ss1292386437 Aug 21, 2014 (142)
8 EVA_EXAC ss1685676543 Apr 01, 2015 (144)
9 ILLUMINA ss1751862463 Sep 08, 2015 (146)
10 ILLUMINA ss1917732318 Feb 12, 2016 (147)
11 ILLUMINA ss1946004441 Feb 12, 2016 (147)
12 ILLUMINA ss1958301765 Feb 12, 2016 (147)
13 HUMAN_LONGEVITY ss2165618222 Dec 20, 2016 (150)
14 GNOMAD ss2731697760 Nov 08, 2017 (151)
15 GNOMAD ss2746390215 Nov 08, 2017 (151)
16 GNOMAD ss2759429921 Nov 08, 2017 (151)
17 AFFY ss2985520990 Nov 08, 2017 (151)
18 ILLUMINA ss3021119528 Nov 08, 2017 (151)
19 ILLUMINA ss3626179578 Oct 11, 2018 (152)
20 ILLUMINA ss3626179579 Oct 11, 2018 (152)
21 ILLUMINA ss3634342178 Oct 11, 2018 (152)
22 ILLUMINA ss3640049537 Oct 11, 2018 (152)
23 ILLUMINA ss3644500413 Oct 11, 2018 (152)
24 ILLUMINA ss3651451451 Oct 11, 2018 (152)
25 ILLUMINA ss3725053346 Jul 12, 2019 (153)
26 ILLUMINA ss3744349416 Jul 12, 2019 (153)
27 ILLUMINA ss3744643135 Jul 12, 2019 (153)
28 EVA ss3746657996 Jul 12, 2019 (153)
29 PAGE_CC ss3770831928 Jul 12, 2019 (153)
30 ILLUMINA ss3772144354 Jul 12, 2019 (153)
31 EVA ss3823639032 Apr 25, 2020 (154)
32 KRGDB ss3894716991 Apr 25, 2020 (154)
33 KOGIC ss3945223397 Apr 25, 2020 (154)
34 TOPMED ss4463202379 Apr 25, 2021 (155)
35 TOMMO_GENOMICS ss5145629913 Apr 25, 2021 (155)
36 1000G_HIGH_COVERAGE ss5243571045 Oct 12, 2022 (156)
37 EVA ss5321112259 Oct 12, 2022 (156)
38 1000G_HIGH_COVERAGE ss5516544215 Oct 12, 2022 (156)
39 TOMMO_GENOMICS ss5670882788 Oct 12, 2022 (156)
40 EVA ss5847550550 Oct 12, 2022 (156)
41 EVA ss5848267361 Oct 12, 2022 (156)
42 EVA ss5909754476 Oct 12, 2022 (156)
43 EVA ss5938140730 Oct 12, 2022 (156)
44 EVA ss5979285528 Oct 12, 2022 (156)
45 1000Genomes NC_000001.10 - 110116624 Oct 11, 2018 (152)
46 1000Genomes_30x NC_000001.11 - 109574002 Oct 12, 2022 (156)
47 ExAC NC_000001.10 - 110116624 Oct 11, 2018 (152)
48 gnomAD - Genomes NC_000001.11 - 109574002 Apr 25, 2021 (155)
49 gnomAD - Exomes NC_000001.10 - 110116624 Jul 12, 2019 (153)
50 GO Exome Sequencing Project NC_000001.10 - 110116624 Oct 11, 2018 (152)
51 KOREAN population from KRGDB NC_000001.10 - 110116624 Apr 25, 2020 (154)
52 Korean Genome Project NC_000001.11 - 109574002 Apr 25, 2020 (154)
53 The PAGE Study NC_000001.11 - 109574002 Jul 12, 2019 (153)
54 8.3KJPN NC_000001.10 - 110116624 Apr 25, 2021 (155)
55 14KJPN NC_000001.11 - 109574002 Oct 12, 2022 (156)
56 TopMed NC_000001.11 - 109574002 Apr 25, 2021 (155)
57 ALFA NC_000001.11 - 109574002 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
3160816, 4884766, 720343, 97663, 1894385, 3599220, ss328849815, ss341980048, ss489756254, ss491297935, ss534952514, ss783571185, ss1292386437, ss1685676543, ss1751862463, ss1917732318, ss1946004441, ss1958301765, ss2731697760, ss2746390215, ss2759429921, ss2985520990, ss3021119528, ss3626179578, ss3626179579, ss3634342178, ss3640049537, ss3644500413, ss3651451451, ss3744349416, ss3744643135, ss3746657996, ss3772144354, ss3823639032, ss3894716991, ss5145629913, ss5321112259, ss5847550550, ss5848267361, ss5938140730, ss5979285528 NC_000001.10:110116623:C:T NC_000001.11:109574001:C:T (self)
4070150, 22363994, 1601398, 53397, 4719892, 26808714, 1349695601, ss2165618222, ss3725053346, ss3770831928, ss3945223397, ss4463202379, ss5243571045, ss5516544215, ss5670882788, ss5909754476 NC_000001.11:109574001:C:T NC_000001.11:109574001: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 rs145097404

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