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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.

rs1486999146

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:16439452 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000007 (1/140282, GnomAD)
A=0.00000 (0/10680, ALFA)
C=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SNHG29 : Intron Variant
SNORD49A : 2KB Upstream Variant
SNORD49B : 2KB Upstream Variant (+ 1 more)
SNORD65 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 10680 G=1.00000 A=0.00000, C=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 G=1.0000 A=0.0000, C=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 G=1.0000 A=0.0000, C=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 G=1.0000 A=0.0000, C=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
Other Sub 466 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A


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 140282 G=0.999993 A=0.000007
gnomAD - Genomes European Sub 75950 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42064 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13662 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 10680 G=1.00000 A=0.00000, C=0.00000
Allele Frequency Aggregator European Sub 6962 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator African Sub 2294 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Other Sub 466 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00, C=0.00
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 17 NC_000017.11:g.16439452G>A
GRCh38.p14 chr 17 NC_000017.11:g.16439452G>C
GRCh37.p13 chr 17 NC_000017.10:g.16342766G>A
GRCh37.p13 chr 17 NC_000017.10:g.16342766G>C
Gene: SNHG29, small nucleolar RNA host gene 29 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SNHG29 transcript variant 2 NR_027158.1:n. N/A Intron Variant
SNHG29 transcript variant 3 NR_027159.1:n. N/A Intron Variant
SNHG29 transcript variant 4 NR_027160.1:n. N/A Intron Variant
SNHG29 transcript variant 5 NR_027161.1:n. N/A Intron Variant
SNHG29 transcript variant 6 NR_027162.1:n. N/A Intron Variant
SNHG29 transcript variant 7 NR_027163.1:n. N/A Intron Variant
SNHG29 transcript variant 8 NR_027164.1:n. N/A Intron Variant
SNHG29 transcript variant 9 NR_027165.1:n. N/A Intron Variant
SNHG29 transcript variant 10 NR_027166.1:n. N/A Intron Variant
SNHG29 transcript variant 11 NR_027167.1:n. N/A Intron Variant
SNHG29 transcript variant 12 NR_027168.2:n. N/A Intron Variant
SNHG29 transcript variant 13 NR_027169.1:n. N/A Intron Variant
SNHG29 transcript variant 14 NR_027170.1:n. N/A Intron Variant
SNHG29 transcript variant 15 NR_027171.1:n. N/A Intron Variant
SNHG29 transcript variant 16 NR_027172.2:n. N/A Intron Variant
SNHG29 transcript variant 17 NR_027173.1:n. N/A Intron Variant
SNHG29 transcript variant 18 NR_027174.1:n. N/A Intron Variant
SNHG29 transcript variant 19 NR_027175.1:n. N/A Intron Variant
SNHG29 transcript variant 20 NR_027176.1:n. N/A Intron Variant
SNHG29 transcript variant 21 NR_027177.1:n. N/A Intron Variant
SNHG29 transcript variant 22 NR_027178.1:n. N/A Intron Variant
SNHG29 transcript variant 23 NR_027179.1:n. N/A Intron Variant
SNHG29 transcript variant 1 NR_027667.1:n. N/A Intron Variant
SNHG29 transcript variant 24 NR_045021.1:n. N/A Intron Variant
SNHG29 transcript variant 25 NR_045022.1:n. N/A Intron Variant
SNHG29 transcript variant 26 NR_045023.1:n. N/A Intron Variant
SNHG29 transcript variant 27 NR_045024.1:n. N/A Intron Variant
SNHG29 transcript variant 28 NR_045025.1:n. N/A Intron Variant
SNHG29 transcript variant 29 NR_045026.1:n. N/A Intron Variant
SNHG29 transcript variant 30 NR_045027.1:n. N/A Intron Variant
SNHG29 transcript variant 31 NR_045028.1:n. N/A Intron Variant
SNHG29 transcript variant 32 NR_045029.1:n. N/A Intron Variant
Gene: SNORD49A, small nucleolar RNA, C/D box 49A (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORD49A transcript NR_002744.1:n. N/A Upstream Transcript Variant
Gene: SNORD49B, small nucleolar RNA, C/D box 49B (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORD49B transcript NR_003043.1:n. N/A Upstream Transcript Variant
Gene: SNORD65, small nucleolar RNA, C/D box 65 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORD65 transcript NR_003054.1: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 G= A C
GRCh38.p14 chr 17 NC_000017.11:g.16439452= NC_000017.11:g.16439452G>A NC_000017.11:g.16439452G>C
GRCh37.p13 chr 17 NC_000017.10:g.16342766= NC_000017.10:g.16342766G>A NC_000017.10:g.16342766G>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#.

2 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2749704610 Nov 08, 2017 (151)
2 GNOMAD ss2948177070 Nov 08, 2017 (151)
3 gnomAD - Genomes NC_000017.11 - 16439452 Apr 27, 2021 (155)
4 ALFA NC_000017.11 - 16439452 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
ss2749704610, ss2948177070 NC_000017.10:16342765:G:A NC_000017.11:16439451:G:A (self)
502681668, 3184567693 NC_000017.11:16439451:G:A NC_000017.11:16439451:G:A (self)
3184567693 NC_000017.11:16439451:G:C NC_000017.11:16439451: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 rs1486999146

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