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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.

rs113383096

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:944101 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.024999 (6617/264690, TOPMED)
C=0.006758 (782/115714, ExAC)
C=0.03574 (2812/78678, PAGE_STUDY) (+ 9 more)
C=0.00113 (50/44314, ALFA)
C=0.00007 (2/28258, 14KJPN)
C=0.00006 (1/16760, 8.3KJPN)
C=0.02414 (314/13006, GO-ESP)
C=0.0212 (136/6404, 1000G_30x)
C=0.0198 (99/5008, 1000G)
C=0.009 (2/216, Qatari)
G=0.5 (4/8, SGDP_PRJ)
C=0.5 (4/8, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SAMD11 : Missense Variant
NOC2L : 500B Downstream 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 44314 G=0.99887 C=0.00113, T=0.00000
European Sub 32778 G=0.99997 C=0.00003, T=0.00000
African Sub 3118 G=0.9917 C=0.0083, T=0.0000
African Others Sub 100 G=1.00 C=0.00, T=0.00
African American Sub 3018 G=0.9914 C=0.0086, T=0.0000
Asian Sub 168 G=1.000 C=0.000, T=0.000
East Asian Sub 112 G=1.000 C=0.000, T=0.000
Other Asian Sub 56 G=1.00 C=0.00, T=0.00
Latin American 1 Sub 496 G=0.986 C=0.014, T=0.000
Latin American 2 Sub 626 G=1.000 C=0.000, T=0.000
South Asian Sub 98 G=1.00 C=0.00, T=0.00
Other Sub 7030 G=0.9977 C=0.0023, T=0.0000


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 G=0.975001 C=0.024999
ExAC Global Study-wide 115714 G=0.993242 C=0.006758
ExAC Europe Sub 70088 G=0.99991 C=0.00009
ExAC Asian Sub 23718 G=0.99979 C=0.00021
ExAC American Sub 11428 G=0.99755 C=0.00245
ExAC African Sub 9632 G=0.9231 C=0.0769
ExAC Other Sub 848 G=0.998 C=0.002
The PAGE Study Global Study-wide 78678 G=0.96426 C=0.03574
The PAGE Study AfricanAmerican Sub 32500 G=0.92646 C=0.07354
The PAGE Study Mexican Sub 10810 G=0.99769 C=0.00231
The PAGE Study Asian Sub 8316 G=1.0000 C=0.0000
The PAGE Study PuertoRican Sub 7916 G=0.9802 C=0.0198
The PAGE Study NativeHawaiian Sub 4532 G=0.9985 C=0.0015
The PAGE Study Cuban Sub 4228 G=0.9875 C=0.0125
The PAGE Study Dominican Sub 3828 G=0.9697 C=0.0303
The PAGE Study CentralAmerican Sub 2450 G=0.9869 C=0.0131
The PAGE Study SouthAmerican Sub 1982 G=0.9899 C=0.0101
The PAGE Study NativeAmerican Sub 1260 G=0.9905 C=0.0095
The PAGE Study SouthAsian Sub 856 G=1.000 C=0.000
Allele Frequency Aggregator Total Global 44314 G=0.99887 C=0.00113, T=0.00000
Allele Frequency Aggregator European Sub 32778 G=0.99997 C=0.00003, T=0.00000
Allele Frequency Aggregator Other Sub 7030 G=0.9977 C=0.0023, T=0.0000
Allele Frequency Aggregator African Sub 3118 G=0.9917 C=0.0083, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 626 G=1.000 C=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 496 G=0.986 C=0.014, T=0.000
Allele Frequency Aggregator Asian Sub 168 G=1.000 C=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 C=0.00, T=0.00
14KJPN JAPANESE Study-wide 28258 G=0.99993 C=0.00007
8.3KJPN JAPANESE Study-wide 16760 G=0.99994 C=0.00006
GO Exome Sequencing Project Global Study-wide 13006 G=0.97586 C=0.02414
GO Exome Sequencing Project European American Sub 8600 G=0.9999 C=0.0001
GO Exome Sequencing Project African American Sub 4406 G=0.9290 C=0.0710
1000Genomes_30x Global Study-wide 6404 G=0.9788 C=0.0212
1000Genomes_30x African Sub 1786 G=0.9267 C=0.0733
1000Genomes_30x Europe Sub 1266 G=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 C=0.0000
1000Genomes_30x American Sub 980 G=0.995 C=0.005
1000Genomes Global Study-wide 5008 G=0.9802 C=0.0198
1000Genomes African Sub 1322 G=0.9281 C=0.0719
1000Genomes East Asian Sub 1008 G=1.0000 C=0.0000
1000Genomes Europe Sub 1006 G=1.0000 C=0.0000
1000Genomes South Asian Sub 978 G=1.000 C=0.000
1000Genomes American Sub 694 G=0.994 C=0.006
Qatari Global Study-wide 216 G=0.991 C=0.009
SGDP_PRJ Global Study-wide 8 G=0.5 C=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.944101G>A
GRCh38.p14 chr 1 NC_000001.11:g.944101G>C
GRCh38.p14 chr 1 NC_000001.11:g.944101G>T
GRCh37.p13 chr 1 NC_000001.10:g.879481G>A
GRCh37.p13 chr 1 NC_000001.10:g.879481G>C
GRCh37.p13 chr 1 NC_000001.10:g.879481G>T
Gene: NOC2L, NOC2 like nucleolar associated transcriptional repressor (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
NOC2L transcript NM_015658.4:c. N/A Downstream Transcript Variant
Gene: SAMD11, sterile alpha motif domain containing 11 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SAMD11 transcript variant 3 NM_152486.4:c.1994G>A G [GGG] > E [GAG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Gly665Glu G (Gly) > E (Glu) Missense Variant
SAMD11 transcript variant 3 NM_152486.4:c.1994G>C G [GGG] > A [GCG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Gly665Ala G (Gly) > A (Ala) Missense Variant
SAMD11 transcript variant 3 NM_152486.4:c.1994G>T G [GGG] > V [GTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Gly665Val G (Gly) > V (Val) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.2483G>A G [GGG] > E [GAG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Gly828Glu G (Gly) > E (Glu) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.2483G>C G [GGG] > A [GCG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Gly828Ala G (Gly) > A (Ala) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.2483G>T G [GGG] > V [GTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Gly828Val G (Gly) > V (Val) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.2486G>A G [GGG] > E [GAG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Gly829Glu G (Gly) > E (Glu) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.2486G>C G [GGG] > A [GCG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Gly829Ala G (Gly) > A (Ala) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.2486G>T G [GGG] > V [GTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Gly829Val G (Gly) > V (Val) 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.

Allele: C (allele ID: 707599 )
ClinVar Accession Disease Names Clinical Significance
RCV000961855.5 not provided Benign
Allele: T (allele ID: 824546 )
ClinVar Accession Disease Names Clinical Significance
RCV001035048.5 not provided Uncertain-Significance
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 G= A C T
GRCh38.p14 chr 1 NC_000001.11:g.944101= NC_000001.11:g.944101G>A NC_000001.11:g.944101G>C NC_000001.11:g.944101G>T
GRCh37.p13 chr 1 NC_000001.10:g.879481= NC_000001.10:g.879481G>A NC_000001.10:g.879481G>C NC_000001.10:g.879481G>T
SAMD11 transcript variant 3 NM_152486.4:c.1994= NM_152486.4:c.1994G>A NM_152486.4:c.1994G>C NM_152486.4:c.1994G>T
SAMD11 transcript NM_152486.3:c.1994= NM_152486.3:c.1994G>A NM_152486.3:c.1994G>C NM_152486.3:c.1994G>T
SAMD11 transcript NM_152486.2:c.1994= NM_152486.2:c.1994G>A NM_152486.2:c.1994G>C NM_152486.2:c.1994G>T
SAMD11 transcript variant 2 NM_001385640.1:c.2486= NM_001385640.1:c.2486G>A NM_001385640.1:c.2486G>C NM_001385640.1:c.2486G>T
SAMD11 transcript variant 1 NM_001385641.1:c.2483= NM_001385641.1:c.2483G>A NM_001385641.1:c.2483G>C NM_001385641.1:c.2483G>T
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Gly665= NP_689699.3:p.Gly665Glu NP_689699.3:p.Gly665Ala NP_689699.3:p.Gly665Val
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Gly829= NP_001372569.1:p.Gly829Glu NP_001372569.1:p.Gly829Ala NP_001372569.1:p.Gly829Val
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Gly828= NP_001372570.1:p.Gly828Glu NP_001372570.1:p.Gly828Ala NP_001372570.1:p.Gly828Val
sterile alpha motif domain-containing protein 11 NP_689699.2:p.Gly665= NP_689699.2:p.Gly665Glu NP_689699.2:p.Gly665Ala NP_689699.2:p.Gly665Val
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#.

50 SubSNP, 16 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 BUSHMAN ss197886513 Jul 04, 2010 (132)
2 1000GENOMES ss218191062 Jul 14, 2010 (132)
3 NHLBI-ESP ss341923451 May 09, 2011 (134)
4 1000GENOMES ss489713647 May 04, 2012 (137)
5 EXOME_CHIP ss491283824 May 04, 2012 (137)
6 ILLUMINA ss533948484 Sep 08, 2015 (146)
7 ILLUMINA ss780783117 Sep 08, 2015 (146)
8 ILLUMINA ss783463496 Sep 08, 2015 (146)
9 JMKIDD_LAB ss1067414263 Aug 21, 2014 (142)
10 JMKIDD_LAB ss1067612794 Aug 21, 2014 (142)
11 1000GENOMES ss1289343214 Aug 21, 2014 (142)
12 EVA_EXAC ss1685218218 Apr 01, 2015 (144)
13 ILLUMINA ss1751937009 Sep 08, 2015 (146)
14 ILLUMINA ss1917720803 Feb 12, 2016 (147)
15 WEILL_CORNELL_DGM ss1917961875 Feb 12, 2016 (147)
16 ILLUMINA ss1945981622 Feb 12, 2016 (147)
17 ILLUMINA ss1958230221 Feb 12, 2016 (147)
18 JJLAB ss2019498917 Sep 14, 2016 (149)
19 HUMAN_LONGEVITY ss2159372162 Dec 20, 2016 (150)
20 GNOMAD ss2730988202 Nov 08, 2017 (151)
21 GNOMAD ss2746169931 Nov 08, 2017 (151)
22 GNOMAD ss2750651358 Nov 08, 2017 (151)
23 AFFY ss2984841029 Nov 08, 2017 (151)
24 ILLUMINA ss3021043231 Nov 08, 2017 (151)
25 ILLUMINA ss3626006685 Oct 11, 2018 (152)
26 ILLUMINA ss3634301852 Oct 11, 2018 (152)
27 ILLUMINA ss3640009218 Oct 11, 2018 (152)
28 ILLUMINA ss3644477494 Oct 11, 2018 (152)
29 ILLUMINA ss3651365283 Oct 11, 2018 (152)
30 ILLUMINA ss3653614782 Oct 11, 2018 (152)
31 ILLUMINA ss3724988152 Jul 12, 2019 (153)
32 ILLUMINA ss3744337229 Jul 12, 2019 (153)
33 ILLUMINA ss3744602784 Jul 12, 2019 (153)
34 PAGE_CC ss3770778588 Jul 12, 2019 (153)
35 ILLUMINA ss3772104547 Jul 12, 2019 (153)
36 KHV_HUMAN_GENOMES ss3798744817 Jul 12, 2019 (153)
37 EVA ss3823541462 Apr 25, 2020 (154)
38 SGDP_PRJ ss3847998760 Apr 25, 2020 (154)
39 EVA ss3986090607 Apr 25, 2021 (155)
40 TOPMED ss4436463847 Apr 25, 2021 (155)
41 TOMMO_GENOMICS ss5142057810 Apr 25, 2021 (155)
42 1000G_HIGH_COVERAGE ss5240867170 Oct 12, 2022 (156)
43 EVA ss5316189517 Oct 12, 2022 (156)
44 HUGCELL_USP ss5442114867 Oct 12, 2022 (156)
45 1000G_HIGH_COVERAGE ss5512493262 Oct 12, 2022 (156)
46 SANFORD_IMAGENETICS ss5624751831 Oct 12, 2022 (156)
47 TOMMO_GENOMICS ss5666198952 Oct 12, 2022 (156)
48 EVA ss5847521248 Oct 12, 2022 (156)
49 EVA ss5906707973 Oct 12, 2022 (156)
50 EVA ss5936584400 Oct 12, 2022 (156)
51 1000Genomes NC_000001.10 - 879481 Oct 11, 2018 (152)
52 1000Genomes_30x NC_000001.11 - 944101 Oct 12, 2022 (156)
53 ExAC NC_000001.10 - 879481 Oct 11, 2018 (152)
54 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 92108 (NC_000001.11:944100:G:C 3369/140186)
Row 92109 (NC_000001.11:944100:G:T 1/140194)

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

Submission ignored due to conflicting rows:
Row 92108 (NC_000001.11:944100:G:C 3369/140186)
Row 92109 (NC_000001.11:944100:G:T 1/140194)

- Apr 25, 2021 (155)
56 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 2533 (NC_000001.10:879480:G:G 242535/242536, NC_000001.10:879480:G:A 1/242536)
Row 2534 (NC_000001.10:879480:G:G 241174/242536, NC_000001.10:879480:G:C 1362/242536)
Row 2535 (NC_000001.10:879480:G:G 242535/242536, NC_000001.10:879480:G:T 1/242536)

- Jul 12, 2019 (153)
57 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 2533 (NC_000001.10:879480:G:G 242535/242536, NC_000001.10:879480:G:A 1/242536)
Row 2534 (NC_000001.10:879480:G:G 241174/242536, NC_000001.10:879480:G:C 1362/242536)
Row 2535 (NC_000001.10:879480:G:G 242535/242536, NC_000001.10:879480:G:T 1/242536)

- Jul 12, 2019 (153)
58 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 2533 (NC_000001.10:879480:G:G 242535/242536, NC_000001.10:879480:G:A 1/242536)
Row 2534 (NC_000001.10:879480:G:G 241174/242536, NC_000001.10:879480:G:C 1362/242536)
Row 2535 (NC_000001.10:879480:G:G 242535/242536, NC_000001.10:879480:G:T 1/242536)

- Jul 12, 2019 (153)
59 GO Exome Sequencing Project NC_000001.10 - 879481 Oct 11, 2018 (152)
60 The PAGE Study NC_000001.11 - 944101 Jul 12, 2019 (153)
61 Qatari NC_000001.10 - 879481 Apr 25, 2020 (154)
62 SGDP_PRJ NC_000001.10 - 879481 Apr 25, 2020 (154)
63 8.3KJPN NC_000001.10 - 879481 Apr 25, 2021 (155)
64 14KJPN NC_000001.11 - 944101 Oct 12, 2022 (156)
65 TopMed NC_000001.11 - 944101 Apr 25, 2021 (155)
66 ALFA NC_000001.11 - 944101 Apr 25, 2021 (155)
67 ClinVar RCV000961855.5 Oct 12, 2022 (156)
68 ClinVar RCV001035048.5 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
ss2730988202 NC_000001.10:879480:G:A NC_000001.11:944100:G:A (self)
ss197886513 NC_000001.9:869343:G:C NC_000001.11:944100:G:C (self)
8105, 4391387, 199, 3805, 15740, 27117, ss218191062, ss341923451, ss489713647, ss491283824, ss533948484, ss780783117, ss783463496, ss1067414263, ss1067612794, ss1289343214, ss1685218218, ss1751937009, ss1917720803, ss1917961875, ss1945981622, ss1958230221, ss2019498917, ss2730988202, ss2746169931, ss2750651358, ss2984841029, ss3021043231, ss3626006685, ss3634301852, ss3640009218, ss3644477494, ss3651365283, ss3653614782, ss3744337229, ss3744602784, ss3772104547, ss3823541462, ss3847998760, ss3986090607, ss5142057810, ss5316189517, ss5624751831, ss5847521248, ss5936584400 NC_000001.10:879480:G:C NC_000001.11:944100:G:C (self)
RCV000961855.5, 19197, 57, 36056, 70182, 3891229283, ss2159372162, ss3724988152, ss3770778588, ss3798744817, ss4436463847, ss5240867170, ss5442114867, ss5512493262, ss5666198952, ss5906707973 NC_000001.11:944100:G:C NC_000001.11:944100:G:C (self)
ss2730988202 NC_000001.10:879480:G:T NC_000001.11:944100:G:T (self)
RCV001035048.5, 3891229283 NC_000001.11:944100:G:T NC_000001.11:944100:G: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 rs113383096

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