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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1491484420

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:6195965-6195966 (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
delAT
Variation Type
Deletion
Frequency
delAT=0.000945 (250/264690, TOPMED)
delAT=0.001000 (140/140032, GnomAD)
delAT=0.00018 (5/28256, 14KJPN) (+ 8 more)
delAT=0.00081 (15/18520, ALFA)
delAT=0.00012 (2/16760, 8.3KJPN)
delAT=0.0006 (4/6404, 1000G_30x)
delAT=0.0006 (3/5008, 1000G)
delAT=0.0002 (1/4480, Estonian)
delAT=0.0016 (6/3854, ALSPAC)
delAT=0.0011 (4/3708, TWINSUK)
delAT=0.002 (2/998, GoNL)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105372255 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 18520 AT=0.99919 =0.00081 0.99838 0.0 0.00162 0
European Sub 14152 AT=0.99936 =0.00064 0.998728 0.0 0.001272 0
African Sub 2898 AT=0.9986 =0.0014 0.997239 0.0 0.002761 0
African Others Sub 114 AT=1.000 =0.000 1.0 0.0 0.0 N/A
African American Sub 2784 AT=0.9986 =0.0014 0.997126 0.0 0.002874 0
Asian Sub 112 AT=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 AT=1.00 =0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 AT=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 AT=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 AT=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 AT=0.99 =0.01 0.979592 0.0 0.020408 0
Other Sub 504 AT=0.998 =0.002 0.996032 0.0 0.003968 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
TopMed Global Study-wide 264690 AT=0.999055 delAT=0.000945
gnomAD - Genomes Global Study-wide 140032 AT=0.999000 delAT=0.001000
gnomAD - Genomes European Sub 75938 AT=0.99897 delAT=0.00103
gnomAD - Genomes African Sub 41844 AT=0.99885 delAT=0.00115
gnomAD - Genomes American Sub 13646 AT=0.99941 delAT=0.00059
gnomAD - Genomes Ashkenazi Jewish Sub 3324 AT=1.0000 delAT=0.0000
gnomAD - Genomes East Asian Sub 3130 AT=0.9994 delAT=0.0006
gnomAD - Genomes Other Sub 2150 AT=0.9981 delAT=0.0019
14KJPN JAPANESE Study-wide 28256 AT=0.99982 delAT=0.00018
Allele Frequency Aggregator Total Global 18520 AT=0.99919 delAT=0.00081
Allele Frequency Aggregator European Sub 14152 AT=0.99936 delAT=0.00064
Allele Frequency Aggregator African Sub 2898 AT=0.9986 delAT=0.0014
Allele Frequency Aggregator Latin American 2 Sub 610 AT=1.000 delAT=0.000
Allele Frequency Aggregator Other Sub 504 AT=0.998 delAT=0.002
Allele Frequency Aggregator Latin American 1 Sub 146 AT=1.000 delAT=0.000
Allele Frequency Aggregator Asian Sub 112 AT=1.000 delAT=0.000
Allele Frequency Aggregator South Asian Sub 98 AT=0.99 delAT=0.01
8.3KJPN JAPANESE Study-wide 16760 AT=0.99988 delAT=0.00012
1000Genomes_30x Global Study-wide 6404 AT=0.9994 delAT=0.0006
1000Genomes_30x African Sub 1786 AT=0.9989 delAT=0.0011
1000Genomes_30x Europe Sub 1266 AT=0.9992 delAT=0.0008
1000Genomes_30x South Asian Sub 1202 AT=0.9992 delAT=0.0008
1000Genomes_30x East Asian Sub 1170 AT=1.0000 delAT=0.0000
1000Genomes_30x American Sub 980 AT=1.000 delAT=0.000
1000Genomes Global Study-wide 5008 AT=0.9994 delAT=0.0006
1000Genomes African Sub 1322 AT=0.9992 delAT=0.0008
1000Genomes East Asian Sub 1008 AT=1.0000 delAT=0.0000
1000Genomes Europe Sub 1006 AT=0.9990 delAT=0.0010
1000Genomes South Asian Sub 978 AT=0.999 delAT=0.001
1000Genomes American Sub 694 AT=1.000 delAT=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 AT=0.9998 delAT=0.0002
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 AT=0.9984 delAT=0.0016
UK 10K study - Twins TWIN COHORT Study-wide 3708 AT=0.9989 delAT=0.0011
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 AT=0.998 delAT=0.002
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 19 NC_000019.10:g.6195965_6195966del
GRCh37.p13 chr 19 NC_000019.9:g.6195976_6195977del
Gene: LOC105372255, uncharacterized LOC105372255 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105372255 transcript variant X1 XR_936282.3:n. N/A Intron Variant
LOC105372255 transcript variant X3 XR_936283.3:n. N/A Intron Variant
LOC105372255 transcript variant X2 XR_936284.4:n. N/A Intron Variant
LOC105372255 transcript variant X4 XR_936285.3: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 AT= delAT
GRCh38.p14 chr 19 NC_000019.10:g.6195965_6195966= NC_000019.10:g.6195965_6195966del
GRCh37.p13 chr 19 NC_000019.9:g.6195976_6195977= NC_000019.9:g.6195976_6195977del
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#.

16 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA-GONL ss994051296 Jan 10, 2018 (151)
2 1000GENOMES ss1377900700 Jan 10, 2018 (151)
3 EVA_UK10K_ALSPAC ss1709105883 Jan 10, 2018 (151)
4 EVA_UK10K_TWINSUK ss1709106062 Jan 10, 2018 (151)
5 GNOMAD ss2960061145 Jan 10, 2018 (151)
6 SWEGEN ss3017031904 Jan 10, 2018 (151)
7 EGCUT_WGS ss3683874907 Jul 13, 2019 (153)
8 EVA_DECODE ss3702269162 Jul 13, 2019 (153)
9 TOPMED ss5066876550 Apr 27, 2021 (155)
10 TOMMO_GENOMICS ss5226561549 Apr 27, 2021 (155)
11 1000G_HIGH_COVERAGE ss5306362448 Oct 16, 2022 (156)
12 HUGCELL_USP ss5499009720 Oct 16, 2022 (156)
13 1000G_HIGH_COVERAGE ss5611713922 Oct 16, 2022 (156)
14 TOMMO_GENOMICS ss5784779606 Oct 16, 2022 (156)
15 EVA ss5927163376 Oct 16, 2022 (156)
16 EVA ss5953330623 Oct 16, 2022 (156)
17 1000Genomes NC_000019.9 - 6195976 Oct 12, 2018 (152)
18 1000Genomes_30x NC_000019.10 - 6195965 Oct 16, 2022 (156)
19 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 6195976 Oct 12, 2018 (152)
20 Genetic variation in the Estonian population NC_000019.9 - 6195976 Oct 12, 2018 (152)
21 gnomAD - Genomes NC_000019.10 - 6195965 Apr 27, 2021 (155)
22 Genome of the Netherlands Release 5 NC_000019.9 - 6195976 Apr 27, 2020 (154)
23 8.3KJPN NC_000019.9 - 6195976 Apr 27, 2021 (155)
24 14KJPN NC_000019.10 - 6195965 Oct 16, 2022 (156)
25 TopMed NC_000019.10 - 6195965 Apr 27, 2021 (155)
26 UK 10K study - Twins NC_000019.9 - 6195976 Oct 12, 2018 (152)
27 ALFA NC_000019.10 - 6195965 Apr 27, 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
75589628, 41887672, 29613155, 18661180, 84530856, 41887672, ss994051296, ss1377900700, ss1709105883, ss1709106062, ss2960061145, ss3017031904, ss3683874907, ss5226561549, ss5953330623 NC_000019.9:6195975:AT: NC_000019.10:6195964:AT: (self)
99239857, 533077671, 118616710, 282422214, 14117664415, ss3702269162, ss5066876550, ss5306362448, ss5499009720, ss5611713922, ss5784779606, ss5927163376 NC_000019.10:6195964:AT: NC_000019.10:6195964:AT: (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 rs1491484420

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.post820+afb47a3d