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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.

rs150003341

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:953875 (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=0.001647 (436/264690, TOPMED)
T=0.000743 (186/250180, GnomAD_exome)
T=0.001604 (225/140278, GnomAD) (+ 7 more)
T=0.000761 (91/119520, ExAC)
T=0.00046 (21/45258, ALFA)
T=0.00154 (20/13006, GO-ESP)
T=0.0031 (20/6404, 1000G_30x)
T=0.0030 (15/5008, 1000G)
C=0.5 (3/6, SGDP_PRJ)
T=0.5 (3/6, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NOC2L : Synonymous 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 61620 C=0.99935 T=0.00065
European Sub 42874 C=1.00000 T=0.00000
African Sub 8818 C=0.9958 T=0.0042
African Others Sub 306 C=0.993 T=0.007
African American Sub 8512 C=0.9959 T=0.0041
Asian Sub 168 C=1.000 T=0.000
East Asian Sub 112 C=1.000 T=0.000
Other Asian Sub 56 C=1.00 T=0.00
Latin American 1 Sub 500 C=0.998 T=0.002
Latin American 2 Sub 628 C=1.000 T=0.000
South Asian Sub 98 C=0.99 T=0.01
Other Sub 8534 C=0.9999 T=0.0001


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=0.998353 T=0.001647
gnomAD - Exomes Global Study-wide 250180 C=0.999257 T=0.000743
gnomAD - Exomes European Sub 134394 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48980 C=0.99786 T=0.00214
gnomAD - Exomes American Sub 34546 C=0.99965 T=0.00035
gnomAD - Exomes African Sub 16136 C=0.99579 T=0.00421
gnomAD - Exomes Ashkenazi Jewish Sub 10022 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6102 C=0.9998 T=0.0002
gnomAD - Genomes Global Study-wide 140278 C=0.998396 T=0.001604
gnomAD - Genomes European Sub 75960 C=0.99996 T=0.00004
gnomAD - Genomes African Sub 42052 C=0.99501 T=0.00499
gnomAD - Genomes American Sub 13658 C=0.99919 T=0.00081
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=0.9995 T=0.0005
ExAC Global Study-wide 119520 C=0.999239 T=0.000761
ExAC Europe Sub 71844 C=1.00000 T=0.00000
ExAC Asian Sub 25098 C=0.99797 T=0.00203
ExAC American Sub 11536 C=0.99983 T=0.00017
ExAC African Sub 10160 C=0.99626 T=0.00374
ExAC Other Sub 882 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 45258 C=0.99954 T=0.00046
Allele Frequency Aggregator European Sub 32784 C=1.00000 T=0.00000
Allele Frequency Aggregator Other Sub 7100 C=0.9999 T=0.0001
Allele Frequency Aggregator African Sub 3980 C=0.9955 T=0.0045
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 C=0.998 T=0.002
Allele Frequency Aggregator Asian Sub 168 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=0.99 T=0.01
GO Exome Sequencing Project Global Study-wide 13006 C=0.99846 T=0.00154
GO Exome Sequencing Project European American Sub 8600 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9955 T=0.0045
1000Genomes_30x Global Study-wide 6404 C=0.9969 T=0.0031
1000Genomes_30x African Sub 1786 C=0.9944 T=0.0056
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=0.9942 T=0.0058
1000Genomes_30x East Asian Sub 1170 C=0.9974 T=0.0026
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9970 T=0.0030
1000Genomes African Sub 1322 C=0.9939 T=0.0061
1000Genomes East Asian Sub 1008 C=0.9990 T=0.0010
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=0.994 T=0.006
1000Genomes American Sub 694 C=1.000 T=0.000
SGDP_PRJ Global Study-wide 6 C=0.5 T=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.953875C>T
GRCh37.p13 chr 1 NC_000001.10:g.889255C>T
Gene: NOC2L, NOC2 like nucleolar associated transcriptional repressor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NOC2L transcript NM_015658.4:c.795G>A S [TCG] > S [TCA] Coding Sequence Variant
nucleolar complex protein 2 homolog NP_056473.3:p.Ser265= S (Ser) > S (Ser) Synonymous 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.953875= NC_000001.11:g.953875C>T
GRCh37.p13 chr 1 NC_000001.10:g.889255= NC_000001.10:g.889255C>T
NOC2L transcript NM_015658.4:c.795= NM_015658.4:c.795G>A
NOC2L transcript NM_015658.3:c.795= NM_015658.3:c.795G>A
nucleolar complex protein 2 homolog NP_056473.3:p.Ser265= NP_056473.3:p.Ser265=
nucleolar complex protein 2 homolog NP_056473.2:p.Ser265= NP_056473.2:p.Ser265=
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#.

23 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss341923570 May 09, 2011 (134)
2 1000GENOMES ss453833713 Sep 17, 2011 (135)
3 1000GENOMES ss489714095 May 04, 2012 (137)
4 WARNICH_LAB ss678260414 Apr 25, 2013 (138)
5 JMKIDD_LAB ss974432443 Aug 21, 2014 (142)
6 1000GENOMES ss1289343733 Aug 21, 2014 (142)
7 HUMAN_LONGEVITY ss2159373215 Dec 20, 2016 (150)
8 GNOMAD ss2746170299 Nov 08, 2017 (151)
9 GNOMAD ss2750652667 Nov 08, 2017 (151)
10 ILLUMINA ss3021043273 Nov 08, 2017 (151)
11 OMUKHERJEE_ADBS ss3646218774 Oct 11, 2018 (152)
12 ILLUMINA ss3651365326 Oct 11, 2018 (152)
13 ILLUMINA ss3724988188 Jul 12, 2019 (153)
14 EVA ss3745722273 Jul 12, 2019 (153)
15 EVA ss3823541659 Apr 25, 2020 (154)
16 SGDP_PRJ ss3847999011 Apr 25, 2020 (154)
17 TOPMED ss4436468037 Apr 25, 2021 (155)
18 1000G_HIGH_COVERAGE ss5240867579 Oct 12, 2022 (156)
19 EVA ss5316190356 Oct 12, 2022 (156)
20 HUGCELL_USP ss5442115280 Oct 12, 2022 (156)
21 1000G_HIGH_COVERAGE ss5512493869 Oct 12, 2022 (156)
22 EVA ss5906708510 Oct 12, 2022 (156)
23 EVA ss5936584626 Oct 12, 2022 (156)
24 1000Genomes NC_000001.10 - 889255 Oct 11, 2018 (152)
25 1000Genomes_30x NC_000001.11 - 953875 Oct 12, 2022 (156)
26 ExAC NC_000001.10 - 889255 Oct 11, 2018 (152)
27 gnomAD - Genomes NC_000001.11 - 953875 Apr 25, 2021 (155)
28 gnomAD - Exomes NC_000001.10 - 889255 Jul 12, 2019 (153)
29 GO Exome Sequencing Project NC_000001.10 - 889255 Oct 11, 2018 (152)
30 SGDP_PRJ NC_000001.10 - 889255 Apr 25, 2020 (154)
31 TopMed NC_000001.11 - 953875 Apr 25, 2021 (155)
32 ALFA NC_000001.11 - 953875 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
8649, 4392261, 3787, 396, 15991, ss341923570, ss453833713, ss489714095, ss678260414, ss974432443, ss1289343733, ss2746170299, ss2750652667, ss3021043273, ss3646218774, ss3651365326, ss3745722273, ss3823541659, ss3847999011, ss5316190356, ss5936584626 NC_000001.10:889254:C:T NC_000001.11:953874:C:T (self)
19804, 95374, 74372, 588217050, ss2159373215, ss3724988188, ss4436468037, ss5240867579, ss5442115280, ss5512493869, ss5906708510 NC_000001.11:953874:C:T NC_000001.11:953874: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 rs150003341

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