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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
chr1:925935 (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=0.000106 (28/264690, TOPMED)
A=0.000241 (60/249146, GnomAD_exome)
A=0.000057 (8/140298, GnomAD) (+ 6 more)
A=0.000209 (25/119486, ExAC)
A=0.00005 (2/44336, ALFA)
A=0.00203 (34/16760, 8.3KJPN)
A=0.0004 (2/5008, 1000G)
A=0.0075 (22/2922, KOREAN)
A=0.0038 (7/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SAMD11 : Synonymous Variant
LOC107985728 : 2KB Upstream 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.925935G>A
GRCh37.p13 chr 1 NC_000001.10:g.861315G>A
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.-7= N/A 5 Prime UTR Variant
SAMD11 transcript variant 1 NM_001385641.1:c.531G>A K [AAG] > K [AAA] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Lys177= K (Lys) > K (Lys) Synonymous Variant
SAMD11 transcript variant 2 NM_001385640.1:c.531G>A K [AAG] > K [AAA] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Lys177= K (Lys) > K (Lys) Synonymous Variant
Gene: LOC107985728, collagen alpha-1(III) chain-like (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC107985728 transcript NR_168405.1:n. N/A Upstream Transcript 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 44336 G=0.99995 A=0.00005
European Sub 32586 G=0.99997 A=0.00003
African Sub 3512 G=1.0000 A=0.0000
African Others Sub 122 G=1.000 A=0.000
African American Sub 3390 G=1.0000 A=0.0000
Asian Sub 168 G=1.000 A=0.000
East Asian Sub 112 G=1.000 A=0.000
Other Asian Sub 56 G=1.00 A=0.00
Latin American 1 Sub 494 G=1.000 A=0.000
Latin American 2 Sub 626 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 6852 G=0.9999 A=0.0001


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=0.999894 A=0.000106
gnomAD - Exomes Global Study-wide 249146 G=0.999759 A=0.000241
gnomAD - Exomes European Sub 133364 G=0.999993 A=0.000007
gnomAD - Exomes Asian Sub 48982 G=0.99882 A=0.00118
gnomAD - Exomes American Sub 34570 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16128 G=0.99994 A=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10004 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6098 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140298 G=0.999943 A=0.000057
gnomAD - Genomes European Sub 75970 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42056 G=0.99995 A=0.00005
gnomAD - Genomes American Sub 13664 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=0.9981 A=0.0019
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
ExAC Global Study-wide 119486 G=0.999791 A=0.000209
ExAC Europe Sub 71878 G=1.00000 A=0.00000
ExAC Asian Sub 25060 G=0.99900 A=0.00100
ExAC American Sub 11510 G=1.00000 A=0.00000
ExAC African Sub 10152 G=1.00000 A=0.00000
ExAC Other Sub 886 G=1.000 A=0.000
8.3KJPN JAPANESE Study-wide 16760 G=0.99797 A=0.00203
1000Genomes Global Study-wide 5008 G=0.9996 A=0.0004
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9980 A=0.0020
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 2922 G=0.9925 A=0.0075
Korean Genome Project KOREAN Study-wide 1832 G=0.9962 A=0.0038

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.925935= NC_000001.11:g.925935G>A
GRCh37.p13 chr 1 NC_000001.10:g.861315= NC_000001.10:g.861315G>A
SAMD11 transcript variant 3 NM_152486.4:c.-7= NM_152486.4:c.-7G>A
SAMD11 transcript NM_152486.3:c.-7= NM_152486.3:c.-7G>A
SAMD11 transcript NM_152486.2:c.-7= NM_152486.2:c.-7G>A
SAMD11 transcript variant 2 NM_001385640.1:c.531= NM_001385640.1:c.531G>A
SAMD11 transcript variant 1 NM_001385641.1:c.531= NM_001385641.1:c.531G>A
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Lys177= NP_001372569.1:p.Lys177=
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Lys177= NP_001372570.1:p.Lys177=

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#.

15 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss487561397 May 04, 2012 (137)
2 1000GENOMES ss1289342265 Aug 21, 2014 (142)
3 BGI ss1558270999 Apr 01, 2015 (144)
4 EVA_EXAC ss1685217238 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2159370249 Dec 20, 2016 (150)
6 TOPMED ss2321509047 Dec 20, 2016 (150)
7 GNOMAD ss2730986803 Nov 08, 2017 (151)
8 GNOMAD ss2746169408 Nov 08, 2017 (151)
9 GNOMAD ss2750648736 Nov 08, 2017 (151)
10 TOPMED ss3066419915 Nov 08, 2017 (151)
11 EVA ss3745721839 Jul 12, 2019 (153)
12 KRGDB ss3892840023 Apr 25, 2020 (154)
13 KOGIC ss3943631529 Apr 25, 2020 (154)
14 TOPMED ss4436456332 Apr 25, 2021 (155)
15 TOMMO_GENOMICS ss5142056656 Apr 25, 2021 (155)
16 1000Genomes NC_000001.10 - 861315 Oct 11, 2018 (152)
17 ExAC NC_000001.10 - 861315 Oct 11, 2018 (152)
18 gnomAD - Genomes NC_000001.11 - 925935 Apr 25, 2021 (155)
19 gnomAD - Exomes NC_000001.10 - 861315 Jul 12, 2019 (153)
20 KOREAN population from KRGDB NC_000001.10 - 861315 Apr 25, 2020 (154)
21 Korean Genome Project NC_000001.11 - 925935 Apr 25, 2020 (154)
22 8.3KJPN NC_000001.10 - 861315 Apr 25, 2021 (155)
23 TopMed NC_000001.11 - 925935 Apr 25, 2021 (155)
24 ALFA NC_000001.11 - 925935 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
ss1558270999 NC_000001.9:851177:G:A NC_000001.11:925934:G:A (self)
7124, 4390333, 1139, 17417, 25963, ss487561397, ss1289342265, ss1685217238, ss2321509047, ss2730986803, ss2746169408, ss2750648736, ss3745721839, ss3892840023, ss5142056656 NC_000001.10:861314:G:A NC_000001.11:925934:G:A (self)
85702, 9530, 31316, 62667, 3508063369, ss2159370249, ss3066419915, ss3943631529, ss4436456332 NC_000001.11:925934:G:A NC_000001.11:925934: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 rs200140498


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