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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
chr1:605161 (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
delC=0.04292 (713/16614, ALFA)
delC=0.0060 (30/5008, 1000G)
delC=0.158 (95/600, NorthernSweden) (+ 1 more)
delC=0.12 (5/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105378947 : Intron Variant
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 1 NC_000001.11:g.605161del
GRCh37.p13 chr 1 NC_000001.10:g.540541del
Gene: LOC105378947, uncharacterized LOC105378947 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105378947 transcript XM_011542538.1:c.1956+279…


N/A Intron Variant

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 16614 C=0.95708 =0.04292
European Sub 12562 C=0.94324 =0.05676
African Sub 2712 C=1.0000 =0.0000
African Others Sub 114 C=1.000 =0.000
African American Sub 2598 C=1.0000 =0.0000
Asian Sub 112 C=1.000 =0.000
East Asian Sub 86 C=1.00 =0.00
Other Asian Sub 26 C=1.00 =0.00
Latin American 1 Sub 116 C=1.000 =0.000
Latin American 2 Sub 572 C=1.000 =0.000
South Asian Sub 86 C=1.00 =0.00
Other Sub 454 C=1.000 =0.000


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
Allele Frequency Aggregator Total Global 16614 C=0.95708 delC=0.04292
Allele Frequency Aggregator European Sub 12562 C=0.94324 delC=0.05676
Allele Frequency Aggregator African Sub 2712 C=1.0000 delC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 572 C=1.000 delC=0.000
Allele Frequency Aggregator Other Sub 454 C=1.000 delC=0.000
Allele Frequency Aggregator Latin American 1 Sub 116 C=1.000 delC=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 delC=0.000
Allele Frequency Aggregator South Asian Sub 86 C=1.00 delC=0.00
1000Genomes Global Study-wide 5008 C=0.9940 delC=0.0060
1000Genomes African Sub 1322 C=0.9985 delC=0.0015
1000Genomes East Asian Sub 1008 C=1.0000 delC=0.0000
1000Genomes Europe Sub 1006 C=0.9771 delC=0.0229
1000Genomes South Asian Sub 978 C=0.996 delC=0.004
1000Genomes American Sub 694 C=0.999 delC=0.001
Northern Sweden ACPOP Study-wide 600 C=0.842 delC=0.158
The Danish reference pan genome Danish Study-wide 40 C=0.88 delC=0.12

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 C= delC
GRCh38.p13 chr 1 NC_000001.11:g.605161= NC_000001.11:g.605161del
GRCh37.p13 chr 1 NC_000001.10:g.540541= NC_000001.10:g.540541del
LOC105378947 transcript XM_011542538.1:c.1956+2794= XM_011542538.1:c.1956+2794del

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#.

9 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss498763781 May 04, 2012 (137)
2 1000GENOMES ss1367645268 Aug 21, 2014 (142)
3 EVA_GENOME_DK ss1573867333 Apr 01, 2015 (144)
4 GNOMAD ss2750620700 Nov 08, 2017 (151)
5 SWEGEN ss2986145430 Nov 08, 2017 (151)
6 MCHAISSO ss3064385976 Nov 08, 2017 (151)
7 TOPMED ss3066362943 Nov 08, 2017 (151)
8 ACPOP ss3726715647 Jul 12, 2019 (153)
9 KHV_HUMAN_GENOMES ss3798742757 Jul 12, 2019 (153)
10 1000Genomes NC_000001.10 - 540541 Oct 11, 2018 (152)
11 The Danish reference pan genome NC_000001.10 - 540541 Apr 25, 2020 (154)
12 Northern Sweden NC_000001.10 - 540541 Jul 12, 2019 (153)
13 ALFA NC_000001.11 - 605161 Apr 25, 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
1411, 120185, 512, ss498763781, ss1367645268, ss1573867333, ss2750620700, ss2986145430, ss3726715647 NC_000001.10:540540:C: NC_000001.11:605160:C: (self)
1154710540, ss3064385976, ss3066362943, ss3798742757 NC_000001.11:605160:C: NC_000001.11:605160:C: (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 rs199511579


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