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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
chr1:604966-604972 (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
Indel Insertion and Deletion
delTGTAT=0.00172 (164/95336, GnomAD)
delTGTAT=0.12669 (2113/16678, 8.3KJPN)
delTGTAT=0.01367 (223/16312, ALFA) (+ 1 more)
delTGTAT=0.17 (7/40, 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.604968_604972del
GRCh37.p13 chr 1 NC_000001.10:g.540348_540352del
Gene: LOC105378947, uncharacterized LOC105378947 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105378947 transcript XM_011542538.1:c.1956+298…


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 16312 ATTGTAT=0.98633 AT=0.01367
European Sub 12060 ATTGTAT=0.98624 AT=0.01376
African Sub 2816 ATTGTAT=0.9801 AT=0.0199
African Others Sub 108 ATTGTAT=0.944 AT=0.056
African American Sub 2708 ATTGTAT=0.9815 AT=0.0185
Asian Sub 108 ATTGTAT=1.000 AT=0.000
East Asian Sub 84 ATTGTAT=1.00 AT=0.00
Other Asian Sub 24 ATTGTAT=1.00 AT=0.00
Latin American 1 Sub 146 ATTGTAT=0.993 AT=0.007
Latin American 2 Sub 610 ATTGTAT=1.000 AT=0.000
South Asian Sub 94 ATTGTAT=1.00 AT=0.00
Other Sub 478 ATTGTAT=1.000 AT=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
gnomAD - Genomes Global Study-wide 95336 ATTGTAT=0.99828 delTGTAT=0.00172
gnomAD - Genomes European Sub 54500 ATTGTAT=0.99996 delTGTAT=0.00004
gnomAD - Genomes African Sub 25404 ATTGTAT=0.99390 delTGTAT=0.00610
gnomAD - Genomes American Sub 9504 ATTGTAT=0.9995 delTGTAT=0.0005
gnomAD - Genomes Ashkenazi Jewish Sub 2632 ATTGTAT=0.9996 delTGTAT=0.0004
gnomAD - Genomes East Asian Sub 1942 ATTGTAT=1.0000 delTGTAT=0.0000
gnomAD - Genomes Other Sub 1354 ATTGTAT=0.9993 delTGTAT=0.0007
8.3KJPN JAPANESE Study-wide 16678 ATTGTAT=0.87331 delTGTAT=0.12669
The Danish reference pan genome Danish Study-wide 40 ATTGTAT=0.82 delTGTAT=0.17

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 ATTGTAT= delTGTAT
GRCh38.p13 chr 1 NC_000001.11:g.604966_604972= NC_000001.11:g.604968_604972del
GRCh37.p13 chr 1 NC_000001.10:g.540346_540352= NC_000001.10:g.540348_540352del
LOC105378947 transcript XM_011542538.1:c.1956+2989= XM_011542538.1:c.1956+2985_1956+2989del

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#.

7 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss287939232 May 04, 2012 (137)
2 1000GENOMES ss498763780 May 04, 2012 (137)
3 EVA_GENOME_DK ss1573867327 Apr 01, 2015 (144)
4 GNOMAD ss2750620675 Nov 08, 2017 (151)
5 SWEGEN ss2986145423 Nov 08, 2017 (151)
6 TOPMED ss3066362896 Nov 08, 2017 (151)
7 TOMMO_GENOMICS ss5142043129 Apr 25, 2021 (155)
8 The Danish reference pan genome NC_000001.10 - 540346 Apr 25, 2020 (154)
9 gnomAD - Genomes NC_000001.11 - 604966 Apr 25, 2021 (155)
10 8.3KJPN NC_000001.10 - 540346 Apr 25, 2021 (155)
11 ALFA NC_000001.11 - 604966 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
ss287939232 NC_000001.9:530208:ATTGT: NC_000001.11:604965:ATTGTAT:AT (self)
120184, 12436, ss498763780, ss1573867327, ss2750620675, ss2986145423, ss5142043129 NC_000001.10:540345:ATTGT: NC_000001.11:604965:ATTGTAT:AT (self)
35643, ss3066362896 NC_000001.11:604965:ATTGT: NC_000001.11:604965:ATTGTAT:AT (self)
7969759396 NC_000001.11:604965:ATTGTAT:AT NC_000001.11:604965:ATTGTAT:AT

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs201534199


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