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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.

rs112858078

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:10214 (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
T=0.00014 (4/28868, GnomAD)
A=0.46913 (8967/19114, 14KJPN)
A=0.47473 (5524/11636, 8.3KJPN) (+ 6 more)
A=0.4547 (2912/6404, 1000G_30x)
A=0.3352 (974/2906, KOREAN)
A=0.316 (174/550, SGDP_PRJ)
A=0.287 (62/216, Qatari)
G=0.0 (0/2, ALFA)
T=0.0 (0/2, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DDX11L10 : 2KB Upstream 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 2 A=1.0 G=0.0, T=0.0
European Sub 2 A=1.0 G=0.0, T=0.0
African Sub 0 A=0 G=0, T=0
African Others Sub 0 A=0 G=0, T=0
African American Sub 0 A=0 G=0, T=0
Asian Sub 0 A=0 G=0, T=0
East Asian Sub 0 A=0 G=0, T=0
Other Asian Sub 0 A=0 G=0, T=0
Latin American 1 Sub 0 A=0 G=0, T=0
Latin American 2 Sub 0 A=0 G=0, T=0
South Asian Sub 0 A=0 G=0, T=0
Other Sub 0 A=0 G=0, T=0


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
gnomAD - Genomes Global Study-wide 28868 A=0.99986 T=0.00014
gnomAD - Genomes European Sub 17606 A=1.00000 T=0.00000
gnomAD - Genomes African Sub 6808 A=0.9997 T=0.0003
gnomAD - Genomes American Sub 2906 A=1.0000 T=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 576 A=1.000 T=0.000
gnomAD - Genomes East Asian Sub 540 A=1.000 T=0.000
gnomAD - Genomes Other Sub 432 A=0.995 T=0.005
14KJPN JAPANESE Study-wide 19114 A=0.46913 G=0.53087
8.3KJPN JAPANESE Study-wide 11636 A=0.47473 G=0.52527
1000Genomes_30x Global Study-wide 6404 A=0.4547 G=0.5453
1000Genomes_30x African Sub 1786 A=0.3819 G=0.6181
1000Genomes_30x Europe Sub 1266 A=0.4929 G=0.5071
1000Genomes_30x South Asian Sub 1202 A=0.4867 G=0.5133
1000Genomes_30x East Asian Sub 1170 A=0.4658 G=0.5342
1000Genomes_30x American Sub 980 A=0.486 G=0.514
KOREAN population from KRGDB KOREAN Study-wide 2906 A=0.3352 G=0.6648, T=0.0000
SGDP_PRJ Global Study-wide 550 A=0.316 G=0.684
Qatari Global Study-wide 216 A=0.287 G=0.713
Allele Frequency Aggregator Total Global 2 A=1.0 G=0.0, T=0.0
Allele Frequency Aggregator European Sub 2 A=1.0 G=0.0, T=0.0
Allele Frequency Aggregator Latin American 1 Sub 0 A=0 G=0, T=0
Allele Frequency Aggregator Latin American 2 Sub 0 A=0 G=0, T=0
Allele Frequency Aggregator South Asian Sub 0 A=0 G=0, T=0
Allele Frequency Aggregator Other Sub 0 A=0 G=0, T=0
Allele Frequency Aggregator African Sub 0 A=0 G=0, T=0
Allele Frequency Aggregator Asian Sub 0 A=0 G=0, T=0
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 16 NC_000016.10:g.10214A>G
GRCh38.p14 chr 16 NC_000016.10:g.10214A>T
GRCh37.p13 chr 16 NC_000016.9:g.60214A>G
GRCh37.p13 chr 16 NC_000016.9:g.60214A>T
Gene: DDX11L10, DEAD/H-box helicase 11 like 10 (pseudogene) (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
DDX11L10 transcript NR_045117.1:n. N/A Upstream Transcript 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 16 NC_000016.10:g.10214= NC_000016.10:g.10214A>G NC_000016.10:g.10214A>T
GRCh37.p13 chr 16 NC_000016.9:g.60214= NC_000016.9:g.60214A>G NC_000016.9:g.60214A>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#.

17 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 BUSHMAN ss201298435 Jul 04, 2010 (132)
2 GMI ss282398905 May 04, 2012 (137)
3 SSMP ss660454540 Apr 25, 2013 (138)
4 DDI ss1427745339 Apr 01, 2015 (144)
5 WEILL_CORNELL_DGM ss1935578010 Feb 12, 2016 (147)
6 GRF ss2701477337 Nov 08, 2017 (151)
7 GNOMAD ss2939119588 Nov 08, 2017 (151)
8 SWEGEN ss3013891409 Nov 08, 2017 (151)
9 CSHL ss3351285179 Nov 08, 2017 (151)
10 SGDP_PRJ ss3883707419 Apr 27, 2020 (154)
11 KRGDB ss3932972722 Apr 27, 2020 (154)
12 TOMMO_GENOMICS ss5217924785 Apr 26, 2021 (155)
13 1000G_HIGH_COVERAGE ss5601803563 Oct 16, 2022 (156)
14 SANFORD_IMAGENETICS ss5658252431 Oct 16, 2022 (156)
15 TOMMO_GENOMICS ss5772247954 Oct 16, 2022 (156)
16 YY_MCH ss5815664931 Oct 16, 2022 (156)
17 EVA ss5845955917 Oct 16, 2022 (156)
18 1000Genomes_30x NC_000016.10 - 10214 Oct 16, 2022 (156)
19 gnomAD - Genomes NC_000016.10 - 10214 Apr 26, 2021 (155)
20 KOREAN population from KRGDB NC_000016.9 - 60214 Apr 27, 2020 (154)
21 Qatari NC_000016.9 - 60214 Apr 27, 2020 (154)
22 SGDP_PRJ NC_000016.9 - 60214 Apr 27, 2020 (154)
23 8.3KJPN NC_000016.9 - 60214 Apr 26, 2021 (155)
24 14KJPN NC_000016.10 - 10214 Oct 16, 2022 (156)
25 ALFA NC_000016.10 - 10214 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss201298435, ss282398905 NC_000016.8:213:A:G NC_000016.10:10213:A:G (self)
40150116, 17619932, 35724399, 75894092, ss660454540, ss1427745339, ss1935578010, ss2701477337, ss2939119588, ss3013891409, ss3351285179, ss3883707419, ss3932972722, ss5217924785, ss5658252431, ss5845955917 NC_000016.9:60213:A:G NC_000016.10:10213:A:G (self)
89329498, 106085058, 7613658516, ss5601803563, ss5772247954, ss5815664931 NC_000016.10:10213:A:G NC_000016.10:10213:A:G (self)
40150116, ss3932972722 NC_000016.9:60213:A:T NC_000016.10:10213:A:T (self)
479806705, 7613658516 NC_000016.10:10213:A:T NC_000016.10:10213: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 rs112858078

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