Skip to main page content
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.

rs201264848

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:939149 (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.

Alleles
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000419 (111/264690, TOPMED)
A=0.000108 (19/175758, GnomAD_exome)
A=0.000385 (54/140232, GnomAD) (+ 5 more)
A=0.00022 (7/31422, ExAC)
A=0.00017 (4/23038, ALFA)
T=0.00006 (1/16760, 8.3KJPN)
A=0.00023 (3/12976, GO-ESP)
A=0.0010 (5/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SAMD11 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.939149G>A
GRCh38.p13 chr 1 NC_000001.11:g.939149G>T
GRCh37.p13 chr 1 NC_000001.10:g.874529G>A
GRCh37.p13 chr 1 NC_000001.10:g.874529G>T
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.1057+20G…

NM_001385640.1:c.1057+20G>A

N/A Intron Variant
SAMD11 transcript variant 1 NM_001385641.1:c.1057+20G…

NM_001385641.1:c.1057+20G>A

N/A Intron Variant
SAMD11 transcript variant 3 NM_152486.4:c.520+20G>A N/A Intron 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

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 23038 G=0.99983 A=0.00017
European Sub 15752 G=1.00000 A=0.00000
African Sub 3492 G=0.9989 A=0.0011
African Others Sub 122 G=0.992 A=0.008
African American Sub 3370 G=0.9991 A=0.0009
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 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 2772 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=0.999581 A=0.000419
gnomAD - Exomes Global Study-wide 175758 G=0.999892 A=0.000108
gnomAD - Exomes European Sub 88068 G=1.00000 A=0.00000
gnomAD - Exomes Asian Sub 37306 G=0.99992 A=0.00008
gnomAD - Exomes American Sub 26398 G=0.99996 A=0.00004
gnomAD - Exomes African Sub 10552 G=0.99877 A=0.00123
gnomAD - Exomes Ashkenazi Jewish Sub 8690 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 4744 G=0.9996 A=0.0004
gnomAD - Genomes Global Study-wide 140232 G=0.999615 A=0.000385
gnomAD - Genomes European Sub 75922 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42030 G=0.99881 A=0.00119
gnomAD - Genomes American Sub 13668 G=0.99985 A=0.00015
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 2154 G=1.0000 A=0.0000
ExAC Global Study-wide 31422 G=0.99978 A=0.00022
ExAC Europe Sub 15436 G=1.00000 A=0.00000
ExAC Asian Sub 10602 G=1.00000 A=0.00000
ExAC African Sub 3818 G=0.9982 A=0.0018
ExAC American Sub 1316 G=1.0000 A=0.0000
ExAC Other Sub 250 G=1.000 A=0.000
8.3KJPN JAPANESE Study-wide 16760 G=0.99994 T=0.00006
GO Exome Sequencing Project Global Study-wide 12976 G=0.99977 A=0.00023
GO Exome Sequencing Project European American Sub 8586 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4390 G=0.9993 A=0.0007
1000Genomes Global Study-wide 5008 G=0.9990 A=0.0010
1000Genomes African Sub 1322 G=0.9962 A=0.0038
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=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
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 T
GRCh38.p13 chr 1 NC_000001.11:g.939149= NC_000001.11:g.939149G>A NC_000001.11:g.939149G>T
GRCh37.p13 chr 1 NC_000001.10:g.874529= NC_000001.10:g.874529G>A NC_000001.10:g.874529G>T
SAMD11 transcript variant 2 NM_001385640.1:c.1057+20= NM_001385640.1:c.1057+20G>A NM_001385640.1:c.1057+20G>T
SAMD11 transcript variant 1 NM_001385641.1:c.1057+20= NM_001385641.1:c.1057+20G>A NM_001385641.1:c.1057+20G>T
SAMD11 transcript NM_152486.2:c.520+20= NM_152486.2:c.520+20G>A NM_152486.2:c.520+20G>T
SAMD11 transcript variant 3 NM_152486.4:c.520+20= NM_152486.4:c.520+20G>A NM_152486.4:c.520+20G>T
SAMD11 transcript variant X1 XM_005244723.1:c.520+20= XM_005244723.1:c.520+20G>A XM_005244723.1:c.520+20G>T
SAMD11 transcript variant X2 XM_005244724.1:c.520+20= XM_005244724.1:c.520+20G>A XM_005244724.1:c.520+20G>T
SAMD11 transcript variant X3 XM_005244725.1:c.520+20= XM_005244725.1:c.520+20G>A XM_005244725.1:c.520+20G>T
SAMD11 transcript variant X4 XM_005244726.1:c.520+20= XM_005244726.1:c.520+20G>A XM_005244726.1:c.520+20G>T
SAMD11 transcript variant X5 XM_005244727.1:c.520+20= XM_005244727.1:c.520+20G>A XM_005244727.1:c.520+20G>T
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#.

15 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss487561438 May 04, 2012 (137)
2 NHLBI-ESP ss712260276 Apr 25, 2013 (138)
3 1000GENOMES ss1289342963 Aug 21, 2014 (142)
4 EVA_EXAC ss1685217512 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2159371563 Dec 20, 2016 (150)
6 TOPMED ss2321510338 Dec 20, 2016 (150)
7 GNOMAD ss2730987203 Nov 08, 2017 (151)
8 GNOMAD ss2746169555 Nov 08, 2017 (151)
9 GNOMAD ss2750650526 Nov 08, 2017 (151)
10 TOPMED ss3066424105 Nov 08, 2017 (151)
11 EVA ss3745722063 Jul 12, 2019 (153)
12 EVA ss3823541348 Apr 25, 2020 (154)
13 EVA ss3986090562 Apr 25, 2021 (155)
14 TOPMED ss4436461308 Apr 25, 2021 (155)
15 TOMMO_GENOMICS ss5142057495 Apr 25, 2021 (155)
16 1000Genomes NC_000001.10 - 874529 Oct 11, 2018 (152)
17 ExAC NC_000001.10 - 874529 Oct 11, 2018 (152)
18 gnomAD - Genomes NC_000001.11 - 939149 Apr 25, 2021 (155)
19 gnomAD - Exomes NC_000001.10 - 874529 Jul 12, 2019 (153)
20 GO Exome Sequencing Project NC_000001.10 - 874529 Oct 11, 2018 (152)
21 8.3KJPN NC_000001.10 - 874529 Apr 25, 2021 (155)
22 TopMed NC_000001.11 - 939149 Apr 25, 2021 (155)
23 ALFA NC_000001.11 - 939149 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
7842, 4390624, 1568, 85, ss487561438, ss712260276, ss1289342963, ss1685217512, ss2321510338, ss2730987203, ss2746169555, ss2750650526, ss3745722063, ss3823541348, ss3986090562 NC_000001.10:874528:G:A NC_000001.11:939148:G:A (self)
89918, 34446, 67643, 11489485462, ss2159371563, ss3066424105, ss4436461308 NC_000001.11:939148:G:A NC_000001.11:939148:G:A (self)
26802, ss5142057495 NC_000001.10:874528:G:T NC_000001.11:939148:G:T
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 rs201264848

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.post596+ae089ad