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dbSNP Short Genetic Variations

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.

rs79003648

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:179097772 (GRCh38.p13) 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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.055831 (14778/264690, TOPMED)
G=0.065772 (9222/140212, GnomAD)
G=0.07941 (1500/18890, ALFA) (+ 14 more)
G=0.03974 (666/16760, 8.3KJPN)
G=0.0429 (215/5008, 1000G)
G=0.1172 (525/4480, Estonian)
G=0.0854 (329/3854, ALSPAC)
G=0.0812 (301/3708, TWINSUK)
G=0.0517 (151/2922, KOREAN)
G=0.0426 (78/1832, Korea1K)
G=0.092 (92/998, GoNL)
G=0.123 (74/600, NorthernSweden)
G=0.064 (34/534, MGP)
G=0.112 (24/214, Vietnamese)
T=0.43 (18/42, SGDP_PRJ)
G=0.12 (5/40, GENOME_DK)
T=0.2 (1/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.179097772T>G
GRCh37.p13 chr 1 NC_000001.10:g.179066907T>G
ABL2 RefSeqGene NG_028242.1:g.136913A>C
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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 T=0.92059 G=0.07941
European Sub 14286 T=0.90277 G=0.09723
African Sub 2946 T=0.9847 G=0.0153
African Others Sub 114 T=0.991 G=0.009
African American Sub 2832 T=0.9845 G=0.0155
Asian Sub 112 T=0.946 G=0.054
East Asian Sub 86 T=0.98 G=0.02
Other Asian Sub 26 T=0.85 G=0.15
Latin American 1 Sub 146 T=0.952 G=0.048
Latin American 2 Sub 610 T=0.970 G=0.030
South Asian Sub 98 T=0.99 G=0.01
Other Sub 692 T=0.951 G=0.049


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 T=0.944169 G=0.055831
gnomAD - Genomes Global Study-wide 140212 T=0.934228 G=0.065772
gnomAD - Genomes European Sub 75918 T=0.90500 G=0.09500
gnomAD - Genomes African Sub 42048 T=0.97933 G=0.02067
gnomAD - Genomes American Sub 13644 T=0.95449 G=0.04551
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9510 G=0.0490
gnomAD - Genomes East Asian Sub 3132 T=0.9266 G=0.0734
gnomAD - Genomes Other Sub 2146 T=0.9408 G=0.0592
8.3KJPN JAPANESE Study-wide 16760 T=0.96026 G=0.03974
1000Genomes Global Study-wide 5008 T=0.9571 G=0.0429
1000Genomes African Sub 1322 T=0.9924 G=0.0076
1000Genomes East Asian Sub 1008 T=0.9276 G=0.0724
1000Genomes Europe Sub 1006 T=0.9056 G=0.0944
1000Genomes South Asian Sub 978 T=0.994 G=0.006
1000Genomes American Sub 694 T=0.955 G=0.045
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.8828 G=0.1172
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9146 G=0.0854
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9188 G=0.0812
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9483 G=0.0517
Korean Genome Project KOREAN Study-wide 1832 T=0.9574 G=0.0426
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.908 G=0.092
Northern Sweden ACPOP Study-wide 600 T=0.877 G=0.123
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.936 G=0.064
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.888 G=0.112
SGDP_PRJ Global Study-wide 42 T=0.43 G=0.57
The Danish reference pan genome Danish Study-wide 40 T=0.88 G=0.12
Siberian Global Study-wide 6 T=0.2 G=0.8
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 T= G
GRCh38.p13 chr 1 NC_000001.11:g.179097772= NC_000001.11:g.179097772T>G
GRCh37.p13 chr 1 NC_000001.10:g.179066907= NC_000001.10:g.179066907T>G
ABL2 RefSeqGene NG_028242.1:g.136913= NG_028242.1:g.136913A>C
TOR3A transcript variant X1 XM_005245445.1:c.944-56= XM_005245445.1:c.944-56T>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#.

40 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss155972293 Dec 01, 2009 (131)
2 1000GENOMES ss230798441 Jul 14, 2010 (132)
3 1000GENOMES ss238431512 Jul 15, 2010 (132)
4 GMI ss276116641 May 04, 2012 (137)
5 GMI ss284182083 Apr 25, 2013 (138)
6 TISHKOFF ss554896606 Apr 25, 2013 (138)
7 SSMP ss648527019 Apr 25, 2013 (138)
8 EVA-GONL ss975859844 Aug 21, 2014 (142)
9 JMKIDD_LAB ss1068398694 Aug 21, 2014 (142)
10 1000GENOMES ss1293604167 Aug 21, 2014 (142)
11 EVA_GENOME_DK ss1574504971 Apr 01, 2015 (144)
12 EVA_DECODE ss1585249308 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1601577276 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1644571309 Apr 01, 2015 (144)
15 EVA_MGP ss1710934123 Apr 01, 2015 (144)
16 JJLAB ss2020063950 Sep 14, 2016 (149)
17 USC_VALOUEV ss2148091478 Dec 20, 2016 (150)
18 HUMAN_LONGEVITY ss2167927140 Dec 20, 2016 (150)
19 TOPMED ss2330478457 Dec 20, 2016 (150)
20 SYSTEMSBIOZJU ss2624540220 Nov 08, 2017 (151)
21 GRF ss2698072886 Nov 08, 2017 (151)
22 GNOMAD ss2763239546 Nov 08, 2017 (151)
23 SWEGEN ss2988024374 Nov 08, 2017 (151)
24 BIOINF_KMB_FNS_UNIBA ss3023791124 Nov 08, 2017 (151)
25 TOPMED ss3096553399 Nov 08, 2017 (151)
26 CSHL ss3343789914 Nov 08, 2017 (151)
27 OMUKHERJEE_ADBS ss3646249425 Oct 11, 2018 (152)
28 EGCUT_WGS ss3655972200 Jul 12, 2019 (153)
29 EVA_DECODE ss3688111469 Jul 12, 2019 (153)
30 ACPOP ss3727632536 Jul 12, 2019 (153)
31 EVA ss3747015223 Jul 12, 2019 (153)
32 KHV_HUMAN_GENOMES ss3800015276 Jul 12, 2019 (153)
33 EVA ss3825581658 Apr 25, 2020 (154)
34 EVA ss3826511154 Apr 25, 2020 (154)
35 SGDP_PRJ ss3850354579 Apr 25, 2020 (154)
36 KRGDB ss3895608483 Apr 25, 2020 (154)
37 KOGIC ss3945986292 Apr 25, 2020 (154)
38 EVA ss3986148933 Apr 25, 2021 (155)
39 TOPMED ss4474296813 Apr 25, 2021 (155)
40 TOMMO_GENOMICS ss5147248309 Apr 25, 2021 (155)
41 1000Genomes NC_000001.10 - 179066907 Oct 11, 2018 (152)
42 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 179066907 Oct 11, 2018 (152)
43 Genetic variation in the Estonian population NC_000001.10 - 179066907 Oct 11, 2018 (152)
44 The Danish reference pan genome NC_000001.10 - 179066907 Apr 25, 2020 (154)
45 gnomAD - Genomes NC_000001.11 - 179097772 Apr 25, 2021 (155)
46 Genome of the Netherlands Release 5 NC_000001.10 - 179066907 Apr 25, 2020 (154)
47 KOREAN population from KRGDB NC_000001.10 - 179066907 Apr 25, 2020 (154)
48 Korean Genome Project NC_000001.11 - 179097772 Apr 25, 2020 (154)
49 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 179066907 Apr 25, 2020 (154)
50 Northern Sweden NC_000001.10 - 179066907 Jul 12, 2019 (153)
51 SGDP_PRJ NC_000001.10 - 179066907 Apr 25, 2020 (154)
52 Siberian NC_000001.10 - 179066907 Apr 25, 2020 (154)
53 8.3KJPN NC_000001.10 - 179066907 Apr 25, 2021 (155)
54 TopMed NC_000001.11 - 179097772 Apr 25, 2021 (155)
55 UK 10K study - Twins NC_000001.10 - 179066907 Oct 11, 2018 (152)
56 A Vietnamese Genetic Variation Database NC_000001.10 - 179066907 Jul 12, 2019 (153)
57 ALFA NC_000001.11 - 179097772 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
ss276116641, ss284182083, ss1585249308 NC_000001.9:177333529:T:G NC_000001.11:179097771:T:G (self)
4419717, 2419533, 1710448, 1777561, 1050744, 2785877, 50875, 917401, 2371559, 607832, 5217616, 2419533, 518709, ss230798441, ss238431512, ss554896606, ss648527019, ss975859844, ss1068398694, ss1293604167, ss1574504971, ss1601577276, ss1644571309, ss1710934123, ss2020063950, ss2148091478, ss2330478457, ss2624540220, ss2698072886, ss2763239546, ss2988024374, ss3343789914, ss3646249425, ss3655972200, ss3727632536, ss3747015223, ss3825581658, ss3826511154, ss3850354579, ss3895608483, ss3986148933, ss5147248309 NC_000001.10:179066906:T:G NC_000001.11:179097771:T:G (self)
31948367, 2364293, 23791975, 37903148, 7190697225, ss2167927140, ss3023791124, ss3096553399, ss3688111469, ss3800015276, ss3945986292, ss4474296813 NC_000001.11:179097771:T:G NC_000001.11:179097771:T:G (self)
ss155972293 NT_004487.19:30555548:T:G NC_000001.11:179097771:T: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 rs79003648

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.post596+ae089ad