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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.

rs1977919

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:15806746 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.05404 (1278/23648, 14KJPN)
G=0.08840 (1258/14230, 8.3KJPN)
G=0.1575 (811/5148, ALFA) (+ 3 more)
G=0.1533 (416/2714, KOREAN)
G=0.049 (9/184, Qatari)
A=0.00 (0/12, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BMS1P22 : Intron Variant
DUXAP8 : Intron 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 5148 A=0.8425 G=0.1575, T=0.0000
European Sub 3582 A=0.8827 G=0.1173, T=0.0000
African Sub 970 A=0.601 G=0.399, T=0.000
African Others Sub 32 A=0.31 G=0.69, T=0.00
African American Sub 938 A=0.611 G=0.389, T=0.000
Asian Sub 60 A=1.00 G=0.00, T=0.00
East Asian Sub 48 A=1.00 G=0.00, T=0.00
Other Asian Sub 12 A=1.00 G=0.00, T=0.00
Latin American 1 Sub 56 A=1.00 G=0.00, T=0.00
Latin American 2 Sub 284 A=1.000 G=0.000, T=0.000
South Asian Sub 42 A=1.00 G=0.00, T=0.00
Other Sub 154 A=0.974 G=0.026, T=0.000


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
14KJPN JAPANESE Study-wide 23648 A=0.94596 G=0.05404
8.3KJPN JAPANESE Study-wide 14230 A=0.91160 G=0.08840
Allele Frequency Aggregator Total Global 5148 A=0.8425 G=0.1575, T=0.0000
Allele Frequency Aggregator European Sub 3582 A=0.8827 G=0.1173, T=0.0000
Allele Frequency Aggregator African Sub 970 A=0.601 G=0.399, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 284 A=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Other Sub 154 A=0.974 G=0.026, T=0.000
Allele Frequency Aggregator Asian Sub 60 A=1.00 G=0.00, T=0.00
Allele Frequency Aggregator Latin American 1 Sub 56 A=1.00 G=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 42 A=1.00 G=0.00, T=0.00
KOREAN population from KRGDB KOREAN Study-wide 2714 A=0.8467 G=0.1533
Qatari Global Study-wide 184 A=0.951 G=0.049
SGDP_PRJ Global Study-wide 12 A=0.00 G=1.00
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 22 NC_000022.11:g.15806746A>G
GRCh38.p14 chr 22 NC_000022.11:g.15806746A>T
GRCh37.p13 chr 22 NC_000022.10:g.16171217T>C
GRCh37.p13 chr 22 NC_000022.10:g.16171217T>A
Gene: DUXAP8, double homeobox A pseudogene 8 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DUXAP8 transcript NR_122113.1:n. N/A Intron Variant
Gene: BMS1P22, BMS1 pseudogene 22 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
BMS1P22 transcript NR_133911.1:n. 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
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 A= G T
GRCh38.p14 chr 22 NC_000022.11:g.15806746= NC_000022.11:g.15806746A>G NC_000022.11:g.15806746A>T
GRCh37.p13 chr 22 NC_000022.10:g.16171217= NC_000022.10:g.16171217T>C NC_000022.10:g.16171217T>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#.

22 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2882887 Jan 12, 2001 (92)
2 SC_JCM ss4028032 Sep 28, 2001 (100)
3 SC_JCM ss6277210 Feb 20, 2003 (111)
4 WI_SSAHASNP ss6654638 Feb 20, 2003 (111)
5 SC_SNP ss8284971 Apr 21, 2003 (114)
6 BCM_SSAHASNP ss11006154 Jul 11, 2003 (116)
7 WI_SSAHASNP ss14393601 Dec 05, 2003 (119)
8 CSHL-HAPMAP ss16923196 Feb 27, 2004 (120)
9 CSHL-HAPMAP ss19497597 Feb 27, 2004 (120)
10 CSHL-HAPMAP ss20141186 Feb 27, 2004 (120)
11 BCMHGSC_JDW ss91864774 Mar 24, 2008 (130)
12 HUMANGENOME_JCVI ss95799120 Feb 06, 2009 (130)
13 ENSEMBL ss144221934 Dec 01, 2009 (131)
14 WEILL_CORNELL_DGM ss1938751351 Feb 12, 2016 (147)
15 SYSTEMSBIOZJU ss2629573869 Nov 08, 2017 (151)
16 GRF ss2704489549 Nov 08, 2017 (151)
17 SWEGEN ss3019016834 Nov 08, 2017 (151)
18 SGDP_PRJ ss3890175283 Apr 27, 2020 (154)
19 KRGDB ss3940533679 Apr 27, 2020 (154)
20 TOMMO_GENOMICS ss5231878026 Apr 26, 2021 (155)
21 SANFORD_IMAGENETICS ss5664167202 Oct 13, 2022 (156)
22 TOMMO_GENOMICS ss5792765014 Oct 13, 2022 (156)
23 KOREAN population from KRGDB NC_000022.10 - 16171217 Apr 27, 2020 (154)
24 Qatari NC_000022.10 - 16171217 Apr 27, 2020 (154)
25 SGDP_PRJ NC_000022.10 - 16171217 Apr 27, 2020 (154)
26 8.3KJPN NC_000022.10 - 16171217 Apr 26, 2021 (155)
27 14KJPN NC_000022.11 - 15806746 Oct 13, 2022 (156)
28 ALFA NC_000022.11 - 15806746 Apr 26, 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).

Associated ID History Updated (Build)
rs62227402 May 27, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss91864774 NC_000022.9:14551216:T:C NC_000022.11:15806745:A:G (self)
47711073, 20793273, 42192263, 89847333, ss1938751351, ss2629573869, ss2704489549, ss3019016834, ss3890175283, ss3940533679, ss5231878026, ss5664167202 NC_000022.10:16171216:T:C NC_000022.11:15806745:A:G (self)
126602118, 2883407287, ss5792765014 NC_000022.11:15806745:A:G NC_000022.11:15806745:A:G (self)
ss6277210, ss6654638, ss8284971, ss11006154, ss14393601, ss16923196, ss19497597, ss20141186 NT_011516.5:121216:T:C NC_000022.11:15806745:A:G (self)
ss2882887, ss4028032, ss95799120, ss144221934 NT_028395.3:121216:T:C NC_000022.11:15806745:A:G (self)
2883407287 NC_000022.11:15806745:A:T NC_000022.11:15806745:A:T (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 rs1977919

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