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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.

rs62635284

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:12783 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/264690, TOPMED)
A=0.01484 (632/42580, GnomAD)
A=0.46289 (7721/16680, 8.3KJPN) (+ 5 more)
A=0.16841 (2712/16104, ALFA)
A=0.4537 (1302/2870, KOREAN)
G=0.393 (214/544, SGDP_PRJ)
G=0.461 (82/178, Qatari)
G=0.42 (17/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DDX11L1 : 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.12783G>A
GRCh38.p13 chr 1 NC_000001.11:g.12783G>C
GRCh37.p13 chr 1 NC_000001.10:g.12783G>A
GRCh37.p13 chr 1 NC_000001.10:g.12783G>C
Gene: DDX11L1, DEAD/H-box helicase 11 like 1 (pseudogene) (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DDX11L1 transcript NR_046018.2: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

ALFA Allele Frequency (New)
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 16104 G=0.83159 A=0.16841, C=0.00000
European Sub 12044 G=0.77524 A=0.22476, C=0.00000
African Sub 2644 G=1.0000 A=0.0000, C=0.0000
African Others Sub 108 G=1.000 A=0.000, C=0.000
African American Sub 2536 G=1.0000 A=0.0000, C=0.0000
Asian Sub 108 G=1.000 A=0.000, C=0.000
East Asian Sub 84 G=1.00 A=0.00, C=0.00
Other Asian Sub 24 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 144 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 604 G=1.000 A=0.000, C=0.000
South Asian Sub 94 G=1.00 A=0.00, C=0.00
Other Sub 466 G=0.989 A=0.011, C=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
TopMed Global Study-wide 264690 G=0.999996 C=0.000004
gnomAD - Genomes Global Study-wide 42580 G=0.98516 A=0.01484
gnomAD - Genomes African Sub 19400 G=0.96918 A=0.03082
gnomAD - Genomes European Sub 17624 G=0.99983 A=0.00017
gnomAD - Genomes American Sub 2976 G=0.9919 A=0.0081
gnomAD - Genomes East Asian Sub 1158 G=0.9991 A=0.0009
gnomAD - Genomes Ashkenazi Jewish Sub 778 G=1.000 A=0.000
gnomAD - Genomes Other Sub 644 G=0.991 A=0.009
8.3KJPN JAPANESE Study-wide 16680 G=0.53711 A=0.46289
KOREAN population from KRGDB KOREAN Study-wide 2870 G=0.5463 A=0.4537
SGDP_PRJ Global Study-wide 544 G=0.393 A=0.607
Qatari Global Study-wide 178 G=0.461 A=0.539
The Danish reference pan genome Danish Study-wide 40 G=0.42 A=0.57
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 C
GRCh38.p13 chr 1 NC_000001.11:g.12783= NC_000001.11:g.12783G>A NC_000001.11:g.12783G>C
GRCh37.p13 chr 1 NC_000001.10:g.12783= NC_000001.10:g.12783G>A NC_000001.10:g.12783G>C
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#.

18 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCMHGSC_JDW ss87152691 Mar 25, 2008 (129)
2 ENSEMBL ss131777737 Dec 01, 2009 (131)
3 ENSEMBL ss132365341 Dec 01, 2009 (131)
4 BCM-HGSC-SUB ss205533187 Jul 04, 2010 (132)
5 EVA_GENOME_DK ss1573850659 Apr 01, 2015 (144)
6 PADH-LAB_SPU ss1713846940 Sep 08, 2015 (146)
7 WEILL_CORNELL_DGM ss1917958096 Feb 12, 2016 (147)
8 JJLAB ss2019497447 Sep 14, 2016 (149)
9 GRF ss2697372877 Nov 08, 2017 (151)
10 GNOMAD ss2750601048 Nov 08, 2017 (151)
11 SWEGEN ss2986141233 Nov 08, 2017 (151)
12 TOPMED ss3066316271 Nov 08, 2017 (151)
13 TOPMED ss3066316272 Nov 08, 2017 (151)
14 OMUKHERJEE_ADBS ss3646217934 Oct 11, 2018 (152)
15 SGDP_PRJ ss3847983136 Apr 25, 2020 (154)
16 KRGDB ss3892822800 Apr 25, 2020 (154)
17 TOPMED ss4436393711 Apr 25, 2021 (155)
18 TOMMO_GENOMICS ss5142030994 Apr 25, 2021 (155)
19 The Danish reference pan genome NC_000001.10 - 12783 Apr 25, 2020 (154)
20 gnomAD - Genomes NC_000001.11 - 12783 Apr 25, 2021 (155)
21 KOREAN population from KRGDB NC_000001.10 - 12783 Apr 25, 2020 (154)
22 Qatari NC_000001.10 - 12783 Apr 25, 2020 (154)
23 SGDP_PRJ NC_000001.10 - 12783 Apr 25, 2020 (154)
24 8.3KJPN NC_000001.10 - 12783 Apr 25, 2021 (155)
25 TopMed NC_000001.11 - 12783 Apr 25, 2021 (155)
26 ALFA NC_000001.11 - 12783 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
ss87152691, ss205533187 NC_000001.9:2645:G:A NC_000001.11:12782:G:A (self)
1357893, 194, 26, 116, 301, ss1573850659, ss1713846940, ss1917958096, ss2019497447, ss2697372877, ss2750601048, ss2986141233, ss3646217934, ss3847983136, ss3892822800, ss5142030994 NC_000001.10:12782:G:A NC_000001.11:12782:G:A (self)
623, 16800625781, ss3066316271 NC_000001.11:12782:G:A NC_000001.11:12782:G:A (self)
ss131777737, ss132365341 NT_077402.2:2782:G:A NC_000001.11:12782:G:A (self)
46, 16800625781, ss3066316272, ss4436393711 NC_000001.11:12782:G:C NC_000001.11:12782:G:C (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 rs62635284

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