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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.

rs79037098

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:942402 (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>A / C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.026998 (7146/264690, TOPMED)
G=0.03448 (2566/74416, GnomAD_exome)
G=0.14864 (4195/28222, 14KJPN) (+ 14 more)
G=0.00237 (61/25770, ALFA)
G=0.14835 (2486/16758, 8.3KJPN)
G=0.0537 (344/6404, 1000G_30x)
G=0.0469 (262/5590, ExAC)
G=0.0549 (275/5008, 1000G)
G=0.0049 (22/4480, Estonian)
G=0.1323 (386/2918, KOREAN)
G=0.1493 (263/1762, Korea1K)
G=0.007 (4/600, NorthernSweden)
G=0.009 (2/216, Qatari)
G=0.112 (24/214, Vietnamese)
C=0.393 (48/122, SGDP_PRJ)
C=0.5 (2/4, Siberian)
G=0.5 (2/4, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SAMD11 : Intron 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 25770 C=0.99763 A=0.00000, G=0.00237
European Sub 19128 C=0.99817 A=0.00000, G=0.00183
African Sub 3306 C=0.9985 A=0.0000, G=0.0015
African Others Sub 114 C=1.000 A=0.000, G=0.000
African American Sub 3192 C=0.9984 A=0.0000, G=0.0016
Asian Sub 118 C=0.983 A=0.000, G=0.017
East Asian Sub 80 C=1.00 A=0.00, G=0.00
Other Asian Sub 38 C=0.95 A=0.00, G=0.05
Latin American 1 Sub 138 C=1.000 A=0.000, G=0.000
Latin American 2 Sub 506 C=1.000 A=0.000, G=0.000
South Asian Sub 94 C=1.00 A=0.00, G=0.00
Other Sub 2480 C=0.9923 A=0.0000, G=0.0077


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=0.973002 G=0.026998
gnomAD - Exomes Global Study-wide 74416 C=0.96552 G=0.03448
gnomAD - Exomes European Sub 30980 C=0.99932 G=0.00068
gnomAD - Exomes Asian Sub 18296 C=0.95447 G=0.04553
gnomAD - Exomes American Sub 15794 C=0.89851 G=0.10149
gnomAD - Exomes Ashkenazi Jewish Sub 5996 C=0.9952 G=0.0048
gnomAD - Exomes Other Sub 2240 C=0.9768 G=0.0232
gnomAD - Exomes African Sub 1110 C=0.9748 G=0.0252
14KJPN JAPANESE Study-wide 28222 C=0.85136 G=0.14864
Allele Frequency Aggregator Total Global 25770 C=0.99763 A=0.00000, G=0.00237
Allele Frequency Aggregator European Sub 19128 C=0.99817 A=0.00000, G=0.00183
Allele Frequency Aggregator African Sub 3306 C=0.9985 A=0.0000, G=0.0015
Allele Frequency Aggregator Other Sub 2480 C=0.9923 A=0.0000, G=0.0077
Allele Frequency Aggregator Latin American 2 Sub 506 C=1.000 A=0.000, G=0.000
Allele Frequency Aggregator Latin American 1 Sub 138 C=1.000 A=0.000, G=0.000
Allele Frequency Aggregator Asian Sub 118 C=0.983 A=0.000, G=0.017
Allele Frequency Aggregator South Asian Sub 94 C=1.00 A=0.00, G=0.00
8.3KJPN JAPANESE Study-wide 16758 C=0.85165 G=0.14835
1000Genomes_30x Global Study-wide 6404 C=0.9460 A=0.0003, G=0.0537
1000Genomes_30x African Sub 1786 C=0.9726 A=0.0011, G=0.0263
1000Genomes_30x Europe Sub 1266 C=0.9984 A=0.0000, G=0.0016
1000Genomes_30x South Asian Sub 1202 C=0.9626 A=0.0000, G=0.0374
1000Genomes_30x East Asian Sub 1170 C=0.8650 A=0.0000, G=0.1350
1000Genomes_30x American Sub 980 C=0.906 A=0.000, G=0.094
ExAC Global Study-wide 5590 C=0.9531 G=0.0469
ExAC Asian Sub 3976 C=0.9432 G=0.0568
ExAC Europe Sub 1308 C=0.9939 G=0.0061
ExAC African Sub 144 C=0.958 G=0.042
ExAC American Sub 98 C=0.79 G=0.21
ExAC Other Sub 64 C=0.98 G=0.02
1000Genomes Global Study-wide 5008 C=0.9451 G=0.0549
1000Genomes African Sub 1322 C=0.9743 G=0.0257
1000Genomes East Asian Sub 1008 C=0.8601 G=0.1399
1000Genomes Europe Sub 1006 C=0.9980 G=0.0020
1000Genomes South Asian Sub 978 C=0.966 G=0.034
1000Genomes American Sub 694 C=0.906 G=0.094
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9951 G=0.0049
KOREAN population from KRGDB KOREAN Study-wide 2918 C=0.8677 G=0.1323
Korean Genome Project KOREAN Study-wide 1762 C=0.8507 G=0.1493
Northern Sweden ACPOP Study-wide 600 C=0.993 G=0.007
Qatari Global Study-wide 216 C=0.991 G=0.009
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.888 G=0.112
SGDP_PRJ Global Study-wide 122 C=0.393 G=0.607
Siberian Global Study-wide 4 C=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.942402C>A
GRCh38.p14 chr 1 NC_000001.11:g.942402C>G
GRCh37.p13 chr 1 NC_000001.10:g.877782C>A
GRCh37.p13 chr 1 NC_000001.10:g.877782C>G
Gene: SAMD11, sterile alpha motif domain containing 11 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SAMD11 transcript variant 2 NM_001385640.1:c.1478-8C>A N/A Intron Variant
SAMD11 transcript variant 1 NM_001385641.1:c.1475-8C>A N/A Intron Variant
SAMD11 transcript variant 3 NM_152486.4:c.986-8C>A 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.

Allele: A (allele ID: 1067655 )
ClinVar Accession Disease Names Clinical Significance
RCV001412837.4 not provided Likely-Benign
Allele: G (allele ID: 1153722 )
ClinVar Accession Disease Names Clinical Significance
RCV001521937.4 not provided 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 C= A G
GRCh38.p14 chr 1 NC_000001.11:g.942402= NC_000001.11:g.942402C>A NC_000001.11:g.942402C>G
GRCh37.p13 chr 1 NC_000001.10:g.877782= NC_000001.10:g.877782C>A NC_000001.10:g.877782C>G
SAMD11 transcript variant 2 NM_001385640.1:c.1478-8= NM_001385640.1:c.1478-8C>A NM_001385640.1:c.1478-8C>G
SAMD11 transcript variant 1 NM_001385641.1:c.1475-8= NM_001385641.1:c.1475-8C>A NM_001385641.1:c.1475-8C>G
SAMD11 transcript NM_152486.2:c.986-8= NM_152486.2:c.986-8C>A NM_152486.2:c.986-8C>G
SAMD11 transcript variant 3 NM_152486.4:c.986-8= NM_152486.4:c.986-8C>A NM_152486.4:c.986-8C>G
SAMD11 transcript variant X1 XM_005244723.1:c.986-8= XM_005244723.1:c.986-8C>A XM_005244723.1:c.986-8C>G
SAMD11 transcript variant X2 XM_005244724.1:c.941-8= XM_005244724.1:c.941-8C>A XM_005244724.1:c.941-8C>G
SAMD11 transcript variant X3 XM_005244725.1:c.938-8= XM_005244725.1:c.938-8C>A XM_005244725.1:c.938-8C>G
SAMD11 transcript variant X4 XM_005244726.1:c.659-8= XM_005244726.1:c.659-8C>A XM_005244726.1:c.659-8C>G
SAMD11 transcript variant X5 XM_005244727.1:c.659-1296= XM_005244727.1:c.659-1296C>A XM_005244727.1:c.659-1296C>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#.

39 SubSNP, 18 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GMI ss154525063 Dec 01, 2009 (131)
2 1000GENOMES ss238115493 Jul 15, 2010 (132)
3 GMI ss275681797 May 04, 2012 (137)
4 1000GENOMES ss489713612 May 04, 2012 (137)
5 SSMP ss647517199 Apr 25, 2013 (138)
6 JMKIDD_LAB ss1067414247 Aug 21, 2014 (142)
7 1000GENOMES ss1289343103 Aug 21, 2014 (142)
8 EVA_EXAC ss1685217751 Apr 01, 2015 (144)
9 WEILL_CORNELL_DGM ss1917961856 Feb 12, 2016 (147)
10 JJLAB ss2019498906 Sep 14, 2016 (149)
11 USC_VALOUEV ss2147485452 Dec 20, 2016 (150)
12 HUMAN_LONGEVITY ss2159371920 Dec 20, 2016 (150)
13 GRF ss2697376411 Nov 08, 2017 (151)
14 GNOMAD ss2730987538 Nov 08, 2017 (151)
15 GNOMAD ss2746169683 Nov 08, 2017 (151)
16 GNOMAD ss2750651038 Nov 08, 2017 (151)
17 SWEGEN ss2986151318 Nov 08, 2017 (151)
18 OMUKHERJEE_ADBS ss3646218748 Oct 11, 2018 (152)
19 EGCUT_WGS ss3654262617 Jul 12, 2019 (153)
20 EVA_DECODE ss3685993988 Jul 12, 2019 (153)
21 ACPOP ss3726717172 Jul 12, 2019 (153)
22 EVA ss3745722098 Jul 12, 2019 (153)
23 KHV_HUMAN_GENOMES ss3798744782 Jul 12, 2019 (153)
24 EVA ss3825548840 Apr 25, 2020 (154)
25 SGDP_PRJ ss3847998715 Apr 25, 2020 (154)
26 KRGDB ss3892840676 Apr 25, 2020 (154)
27 KOGIC ss3943632029 Apr 25, 2020 (154)
28 EVA ss3986090573 Apr 25, 2021 (155)
29 TOPMED ss4436462869 Apr 25, 2021 (155)
30 TOMMO_GENOMICS ss5142057687 Apr 25, 2021 (155)
31 1000G_HIGH_COVERAGE ss5240867082 Oct 12, 2022 (156)
32 EVA ss5316189317 Oct 12, 2022 (156)
33 HUGCELL_USP ss5442114781 Oct 12, 2022 (156)
34 1000G_HIGH_COVERAGE ss5512493114 Oct 12, 2022 (156)
35 SANFORD_IMAGENETICS ss5624751790 Oct 12, 2022 (156)
36 TOMMO_GENOMICS ss5666198802 Oct 12, 2022 (156)
37 YY_MCH ss5800244810 Oct 12, 2022 (156)
38 EVA ss5906707863 Oct 12, 2022 (156)
39 EVA ss5936584358 Oct 12, 2022 (156)
40 1000Genomes NC_000001.10 - 877782 Oct 11, 2018 (152)
41 1000Genomes_30x NC_000001.11 - 942402 Oct 12, 2022 (156)
42 Genetic variation in the Estonian population NC_000001.10 - 877782 Oct 11, 2018 (152)
43 ExAC NC_000001.10 - 877782 Oct 11, 2018 (152)
44 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 91279 (NC_000001.11:942401:C:A 15/140208)
Row 91280 (NC_000001.11:942401:C:G 2762/140200)

- Apr 25, 2021 (155)
45 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 91279 (NC_000001.11:942401:C:A 15/140208)
Row 91280 (NC_000001.11:942401:C:G 2762/140200)

- Apr 25, 2021 (155)
46 gnomAD - Exomes NC_000001.10 - 877782 Jul 12, 2019 (153)
47 KOREAN population from KRGDB NC_000001.10 - 877782 Apr 25, 2020 (154)
48 Korean Genome Project NC_000001.11 - 942402 Apr 25, 2020 (154)
49 Northern Sweden NC_000001.10 - 877782 Jul 12, 2019 (153)
50 Qatari NC_000001.10 - 877782 Apr 25, 2020 (154)
51 SGDP_PRJ NC_000001.10 - 877782 Apr 25, 2020 (154)
52 Siberian NC_000001.10 - 877782 Apr 25, 2020 (154)
53 8.3KJPN NC_000001.10 - 877782 Apr 25, 2021 (155)
54 14KJPN NC_000001.11 - 942402 Oct 12, 2022 (156)
55 TopMed NC_000001.11 - 942402 Apr 25, 2021 (155)
56 A Vietnamese Genetic Variation Database NC_000001.10 - 877782 Jul 12, 2019 (153)
57 ALFA NC_000001.11 - 942402 Apr 25, 2021 (155)
58 ClinVar RCV001412837.4 Oct 12, 2022 (156)
59 ClinVar RCV001521937.4 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
ss2730987538, ss2746169683, ss2750651038 NC_000001.10:877781:C:A NC_000001.11:942401:C:A (self)
RCV001412837.4, 19049, 6836658093, ss2159371920, ss5512493114 NC_000001.11:942401:C:A NC_000001.11:942401:C:A (self)
ss275681797 NC_000001.9:867644:C:G NC_000001.11:942401:C:G (self)
7989, 865, 4390887, 1844, 18070, 2037, 3786, 15695, 1806, 26994, 387, ss238115493, ss489713612, ss647517199, ss1067414247, ss1289343103, ss1685217751, ss1917961856, ss2019498906, ss2147485452, ss2697376411, ss2730987538, ss2746169683, ss2750651038, ss2986151318, ss3646218748, ss3654262617, ss3726717172, ss3745722098, ss3825548840, ss3847998715, ss3892840676, ss3986090573, ss5142057687, ss5316189317, ss5624751790, ss5936584358 NC_000001.10:877781:C:G NC_000001.11:942401:C:G (self)
RCV001521937.4, 19049, 10030, 35906, 69204, 6836658093, ss2159371920, ss3685993988, ss3798744782, ss3943632029, ss4436462869, ss5240867082, ss5442114781, ss5512493114, ss5666198802, ss5800244810, ss5906707863 NC_000001.11:942401:C:G NC_000001.11:942401:C:G (self)
ss154525063 NT_004350.19:356413:C:G NC_000001.11:942401:C: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 rs79037098

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