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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
chr16:40879 (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=0.066931 (8421/125816, GnomAD)
A=0.06137 (728/11862, ALFA)
A=0.1032 (517/5008, 1000G) (+ 5 more)
A=0.0360 (105/2920, KOREAN)
A=0.008 (5/600, NorthernSweden)
A=0.098 (21/214, Qatari)
T=0.50 (24/48, SGDP_PRJ)
A=0.50 (24/48, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
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 16 NC_000016.10:g.40879T>A
GRCh37.p13 chr 16 NC_000016.9:g.90879T>A

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 T=0.93863 A=0.06137
European Sub 7618 T=0.9798 A=0.0202
African Sub 2816 T=0.8182 A=0.1818
African Others Sub 108 T=0.824 A=0.176
African American Sub 2708 T=0.8179 A=0.1821
Asian Sub 108 T=1.000 A=0.000
East Asian Sub 84 T=1.00 A=0.00
Other Asian Sub 24 T=1.00 A=0.00
Latin American 1 Sub 146 T=0.911 A=0.089
Latin American 2 Sub 610 T=0.980 A=0.020
South Asian Sub 94 T=1.00 A=0.00
Other Sub 470 T=0.921 A=0.079


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
gnomAD - Genomes Global Study-wide 125816 T=0.933069 A=0.066931
gnomAD - Genomes European Sub 67006 T=0.98440 A=0.01560
gnomAD - Genomes African Sub 39172 T=0.82886 A=0.17114
gnomAD - Genomes American Sub 11814 T=0.96436 A=0.03564
gnomAD - Genomes Ashkenazi Jewish Sub 3124 T=0.9526 A=0.0474
gnomAD - Genomes East Asian Sub 2800 T=0.9996 A=0.0004
gnomAD - Genomes Other Sub 1900 T=0.9463 A=0.0537
1000Genomes Global Study-wide 5008 T=0.8968 A=0.1032
1000Genomes African Sub 1322 T=0.7882 A=0.2118
1000Genomes East Asian Sub 1008 T=0.9544 A=0.0456
1000Genomes Europe Sub 1006 T=0.9364 A=0.0636
1000Genomes South Asian Sub 978 T=0.925 A=0.075
1000Genomes American Sub 694 T=0.922 A=0.078
KOREAN population from KRGDB KOREAN Study-wide 2920 T=0.9640 A=0.0360
Northern Sweden ACPOP Study-wide 600 T=0.992 A=0.008
Qatari Global Study-wide 214 T=0.902 A=0.098
SGDP_PRJ Global Study-wide 48 T=0.50 A=0.50

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 T= A
GRCh38.p13 chr 16 NC_000016.10:g.40879= NC_000016.10:g.40879T>A
GRCh37.p13 chr 16 NC_000016.9:g.90879= NC_000016.9:g.90879T>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#.

17 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 BL ss255419403 May 09, 2011 (134)
2 GMI ss282399012 May 04, 2012 (137)
3 EVA-GONL ss992173267 Aug 21, 2014 (142)
4 1000GENOMES ss1354950956 Aug 21, 2014 (142)
5 WEILL_CORNELL_DGM ss1935578310 Feb 12, 2016 (147)
6 HUMAN_LONGEVITY ss2136312805 Dec 20, 2016 (150)
7 GRF ss2701477560 Nov 08, 2017 (151)
8 GNOMAD ss2939123207 Nov 08, 2017 (151)
9 SWEGEN ss3013892131 Nov 08, 2017 (151)
10 TOPMED ss3237331791 Nov 08, 2017 (151)
11 CSHL ss3351285358 Nov 08, 2017 (151)
12 EVA_DECODE ss3698629153 Jul 13, 2019 (153)
13 ACPOP ss3741245910 Jul 13, 2019 (153)
14 KHV_HUMAN_GENOMES ss3818854502 Jul 13, 2019 (153)
15 EVA ss3834421839 Apr 27, 2020 (154)
16 SGDP_PRJ ss3883708557 Apr 27, 2020 (154)
17 KRGDB ss3932973759 Apr 27, 2020 (154)
18 1000Genomes NC_000016.9 - 90879 Oct 12, 2018 (152)
19 gnomAD - Genomes NC_000016.10 - 40879 Apr 26, 2021 (155)
20 KOREAN population from KRGDB NC_000016.9 - 90879 Apr 27, 2020 (154)
21 Northern Sweden NC_000016.9 - 90879 Jul 13, 2019 (153)
22 Qatari NC_000016.9 - 90879 Apr 27, 2020 (154)
23 SGDP_PRJ NC_000016.9 - 90879 Apr 27, 2020 (154)
24 ALFA NC_000016.10 - 40879 Apr 26, 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
ss255419403, ss282399012 NC_000016.8:30878:T:A NC_000016.10:40878:T:A (self)
68075544, 40151153, 14530775, 17620232, 35725537, ss992173267, ss1354950956, ss1935578310, ss2701477560, ss2939123207, ss3013892131, ss3351285358, ss3741245910, ss3834421839, ss3883708557, ss3932973759 NC_000016.9:90878:T:A NC_000016.10:40878:T:A (self)
479813544, 7546772712, ss2136312805, ss3237331791, ss3698629153, ss3818854502 NC_000016.10:40878:T:A NC_000016.10:40878:T: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 rs142770258


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