Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs199902603

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:939460 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000026 (7/264690, TOPMED)
A=0.000072 (17/236528, GnomAD_exome)
A=0.000016 (2/127560, GnomAD) (+ 7 more)
A=0.000100 (11/110312, ExAC)
A=0.00006 (2/35236, ALFA)
A=0.00152 (43/28256, 14KJPN)
A=0.00161 (27/16760, 8.3KJPN)
A=0.0002 (1/5008, 1000G)
A=0.0014 (4/2918, KOREAN)
A=0.0022 (4/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SAMD11 : 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 35236 G=0.99994 A=0.00006
European Sub 26440 G=0.99992 A=0.00008
African Sub 2918 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 2804 G=1.0000 A=0.0000
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 496 G=1.000 A=0.000
Latin American 2 Sub 628 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 4544 G=1.0000 A=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=0.999974 A=0.000026
gnomAD - Exomes Global Study-wide 236528 G=0.999928 A=0.000072
gnomAD - Exomes European Sub 125600 G=0.999960 A=0.000040
gnomAD - Exomes Asian Sub 47126 G=0.99975 A=0.00025
gnomAD - Exomes American Sub 32798 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 15768 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9526 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 5710 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 127560 G=0.999984 A=0.000016
gnomAD - Genomes European Sub 66424 G=0.99997 A=0.00003
gnomAD - Genomes African Sub 40496 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 12638 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3122 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 2940 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1940 G=1.0000 A=0.0000
ExAC Global Study-wide 110312 G=0.999900 A=0.000100
ExAC Europe Sub 66492 G=0.99994 A=0.00006
ExAC Asian Sub 22572 G=0.99969 A=0.00031
ExAC American Sub 10970 G=1.00000 A=0.00000
ExAC African Sub 9496 G=1.0000 A=0.0000
ExAC Other Sub 782 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 35236 G=0.99994 A=0.00006
Allele Frequency Aggregator European Sub 26440 G=0.99992 A=0.00008
Allele Frequency Aggregator Other Sub 4544 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2918 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 496 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
14KJPN JAPANESE Study-wide 28256 G=0.99848 A=0.00152
8.3KJPN JAPANESE Study-wide 16760 G=0.99839 A=0.00161
1000Genomes Global Study-wide 5008 G=0.9998 A=0.0002
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2918 G=0.9986 A=0.0014
Korean Genome Project KOREAN Study-wide 1832 G=0.9978 A=0.0022
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.939460G>A
GRCh37.p13 chr 1 NC_000001.10:g.874840G>A
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.1198+48G…

NM_001385640.1:c.1198+48G>A

N/A Intron Variant
SAMD11 transcript variant 1 NM_001385641.1:c.1195+48G…

NM_001385641.1:c.1195+48G>A

N/A Intron Variant
SAMD11 transcript variant 3 NM_152486.4:c.706G>A D [GAT] > N [AAT] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Asp236Asn D (Asp) > N (Asn) 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 G= A
GRCh38.p14 chr 1 NC_000001.11:g.939460= NC_000001.11:g.939460G>A
GRCh37.p13 chr 1 NC_000001.10:g.874840= NC_000001.10:g.874840G>A
SAMD11 transcript variant 3 NM_152486.4:c.706= NM_152486.4:c.706G>A
SAMD11 transcript NM_152486.3:c.706= NM_152486.3:c.706G>A
SAMD11 transcript NM_152486.2:c.706= NM_152486.2:c.706G>A
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Asp236= NP_689699.3:p.Asp236Asn
SAMD11 transcript variant 2 NM_001385640.1:c.1198+48= NM_001385640.1:c.1198+48G>A
SAMD11 transcript variant 1 NM_001385641.1:c.1195+48= NM_001385641.1:c.1195+48G>A
sterile alpha motif domain-containing protein 11 NP_689699.2:p.Asp236= NP_689699.2:p.Asp236Asn
SAMD11 transcript variant X2 XM_005244724.1:c.661+48= XM_005244724.1:c.661+48G>A
SAMD11 transcript variant X3 XM_005244725.1:c.658+48= XM_005244725.1:c.658+48G>A
SAMD11 transcript variant X4 XM_005244726.1:c.658+48= XM_005244726.1:c.658+48G>A
SAMD11 transcript variant X5 XM_005244727.1:c.658+48= XM_005244727.1:c.658+48G>A
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#.

14 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss488646435 May 04, 2012 (137)
2 1000GENOMES ss1289342984 Aug 21, 2014 (142)
3 EVA_EXAC ss1685217585 Apr 01, 2015 (144)
4 HUMAN_LONGEVITY ss2159371594 Dec 20, 2016 (150)
5 GNOMAD ss2730987300 Nov 08, 2017 (151)
6 EVA ss3745722072 Jul 12, 2019 (153)
7 KRGDB ss3892840605 Apr 25, 2020 (154)
8 KOGIC ss3943631969 Apr 25, 2020 (154)
9 GNOMAD ss3986941233 Apr 25, 2021 (155)
10 TOPMED ss4436461433 Apr 25, 2021 (155)
11 TOMMO_GENOMICS ss5142057516 Apr 25, 2021 (155)
12 EVA ss5316189086 Oct 12, 2022 (156)
13 TOMMO_GENOMICS ss5666198566 Oct 12, 2022 (156)
14 EVA ss5906707739 Oct 12, 2022 (156)
15 1000Genomes NC_000001.10 - 874840 Oct 11, 2018 (152)
16 ExAC NC_000001.10 - 874840 Oct 11, 2018 (152)
17 gnomAD - Genomes NC_000001.11 - 939460 Apr 25, 2021 (155)
18 gnomAD - Exomes NC_000001.10 - 874840 Jul 12, 2019 (153)
19 KOREAN population from KRGDB NC_000001.10 - 874840 Apr 25, 2020 (154)
20 Korean Genome Project NC_000001.11 - 939460 Apr 25, 2020 (154)
21 8.3KJPN NC_000001.10 - 874840 Apr 25, 2021 (155)
22 14KJPN NC_000001.11 - 939460 Oct 12, 2022 (156)
23 TopMed NC_000001.11 - 939460 Apr 25, 2021 (155)
24 ALFA NC_000001.11 - 939460 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
7863, 4390703, 1684, 17999, 26823, ss488646435, ss1289342984, ss1685217585, ss2730987300, ss3745722072, ss3892840605, ss5142057516, ss5316189086 NC_000001.10:874839:G:A NC_000001.11:939459:G:A (self)
90027, 9970, 35670, 67768, 5133711171, ss2159371594, ss3943631969, ss3986941233, ss4436461433, ss5666198566, ss5906707739 NC_000001.11:939459:G:A NC_000001.11:939459:G:A (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 rs199902603

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