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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:931108 (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.

Variation Type
SNV Single Nucleotide Variation
A=0.000038 (10/264690, TOPMED)
A=0.000257 (64/249416, GnomAD_exome)
A=0.000036 (5/140220, GnomAD) (+ 3 more)
A=0.000225 (27/119810, ExAC)
A=0.00008 (1/11862, ALFA)
A=0.0006 (3/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SAMD11 : Intron Variant
0 citations
Genomic View
See rs on genome

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.931108G>A
GRCh37.p13 chr 1 NC_000001.10:g.866488G>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.842+19G>A N/A Intron Variant
SAMD11 transcript variant 1 NM_001385641.1:c.842+19G>A N/A Intron Variant
SAMD11 transcript variant 3 NM_152486.4:c.305+19G>A N/A Intron Variant

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 11862 G=0.99992 A=0.00008
European Sub 7618 G=1.0000 A=0.0000
African Sub 2816 G=1.0000 A=0.0000
African Others Sub 108 G=1.000 A=0.000
African American Sub 2708 G=1.0000 A=0.0000
Asian Sub 108 G=1.000 A=0.000
East Asian Sub 84 G=1.00 A=0.00
Other Asian Sub 24 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 94 G=0.99 A=0.01
Other Sub 470 G=1.000 A=0.000


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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.999962 A=0.000038
gnomAD - Exomes Global Study-wide 249416 G=0.999743 A=0.000257
gnomAD - Exomes European Sub 133692 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 48960 G=0.99875 A=0.00125
gnomAD - Exomes American Sub 34518 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16142 G=0.99994 A=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10012 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6092 G=0.9997 A=0.0003
gnomAD - Genomes Global Study-wide 140220 G=0.999964 A=0.000036
gnomAD - Genomes European Sub 75922 G=0.99996 A=0.00004
gnomAD - Genomes African Sub 42030 G=0.99998 A=0.00002
gnomAD - Genomes American Sub 13658 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2152 G=1.0000 A=0.0000
ExAC Global Study-wide 119810 G=0.999775 A=0.000225
ExAC Europe Sub 72110 G=1.00000 A=0.00000
ExAC Asian Sub 25086 G=0.99896 A=0.00104
ExAC American Sub 11520 G=1.00000 A=0.00000
ExAC African Sub 10204 G=0.99990 A=0.00010
ExAC Other Sub 890 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9994 A=0.0006
1000Genomes African Sub 1322 G=0.9992 A=0.0008
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=0.998 A=0.002
1000Genomes American Sub 694 G=1.000 A=0.000

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.p13 chr 1 NC_000001.11:g.931108= NC_000001.11:g.931108G>A
GRCh37.p13 chr 1 NC_000001.10:g.866488= NC_000001.10:g.866488G>A
SAMD11 transcript variant 2 NM_001385640.1:c.842+19= NM_001385640.1:c.842+19G>A
SAMD11 transcript variant 1 NM_001385641.1:c.842+19= NM_001385641.1:c.842+19G>A
SAMD11 transcript NM_152486.2:c.305+19= NM_152486.2:c.305+19G>A
SAMD11 transcript variant 3 NM_152486.4:c.305+19= NM_152486.4:c.305+19G>A
SAMD11 transcript variant X1 XM_005244723.1:c.305+19= XM_005244723.1:c.305+19G>A
SAMD11 transcript variant X2 XM_005244724.1:c.305+19= XM_005244724.1:c.305+19G>A
SAMD11 transcript variant X3 XM_005244725.1:c.305+19= XM_005244725.1:c.305+19G>A
SAMD11 transcript variant X4 XM_005244726.1:c.305+19= XM_005244726.1:c.305+19G>A
SAMD11 transcript variant X5 XM_005244727.1:c.305+19= XM_005244727.1:c.305+19G>A

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#.

9 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss487561411 May 04, 2012 (137)
2 CLINSEQ_SNP ss491581631 May 04, 2012 (137)
3 1000GENOMES ss1289342580 Aug 21, 2014 (142)
4 EVA_EXAC ss1685217365 Apr 01, 2015 (144)
5 GNOMAD ss2730987012 Nov 08, 2017 (151)
6 GNOMAD ss2746169484 Nov 08, 2017 (151)
7 GNOMAD ss2750649476 Nov 08, 2017 (151)
8 TOPMED ss3066421520 Nov 08, 2017 (151)
9 TOPMED ss4436458430 Apr 25, 2021 (155)
10 1000Genomes NC_000001.10 - 866488 Oct 11, 2018 (152)
11 ExAC NC_000001.10 - 866488 Oct 11, 2018 (152)
12 gnomAD - Genomes NC_000001.11 - 931108 Apr 25, 2021 (155)
13 gnomAD - Exomes NC_000001.10 - 866488 Jul 12, 2019 (153)
14 TopMed NC_000001.11 - 931108 Apr 25, 2021 (155)
15 ALFA NC_000001.11 - 931108 Apr 25, 2021 (155)

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
ss491581631 NC_000001.9:856350:G:A NC_000001.11:931107:G:A (self)
7439, 4390469, 1354, ss487561411, ss1289342580, ss1685217365, ss2730987012, ss2746169484, ss2750649476 NC_000001.10:866487:G:A NC_000001.11:931107:G:A (self)
87449, 64765, 8355519159, ss3066421520, ss4436458430 NC_000001.11:931107:G:A NC_000001.11:931107:G:A (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs200139083


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