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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.

rs1486284351

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:3560005 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000042 (11/264690, TOPMED)
T=0.000021 (3/140134, GnomAD)
T=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNASEH1-DT : Intron Variant
RNASEH1 : 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 14050 C=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 C=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 C=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 496 C=1.000 T=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
TopMed Global Study-wide 264690 C=0.999958 T=0.000042
gnomAD - Genomes Global Study-wide 140134 C=0.999979 T=0.000021
gnomAD - Genomes European Sub 75910 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 41964 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13656 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=0.9990 T=0.0010
gnomAD - Genomes Other Sub 2148 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 14050 C=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 9690 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2898 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Other Sub 496 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=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 2 NC_000002.12:g.3560005C>T
GRCh37.p13 chr 2 NC_000002.11:g.3607595C>T
RNASEH1 RefSeqGene (LRG_1090) NG_051310.1:g.3367G>A
Gene: RNASEH1, ribonuclease H1 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
RNASEH1 transcript variant 1 NM_001286834.3:c. N/A Upstream Transcript Variant
RNASEH1 transcript variant 2 NM_001286837.3:c. N/A Upstream Transcript Variant
RNASEH1 transcript variant 6 NM_001378271.1:c. N/A Upstream Transcript Variant
RNASEH1 transcript variant 7 NM_001378272.1:c. N/A Upstream Transcript Variant
RNASEH1 transcript variant 8 NM_001378273.1:c. N/A Upstream Transcript Variant
RNASEH1 transcript variant 1 NM_002936.6:c. N/A Upstream Transcript Variant
RNASEH1 transcript variant 3 NR_148532.2:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant 4 NR_148533.2:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant 5 NR_148534.2:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant 9 NR_165465.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant 10 NR_165466.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant 11 NR_165467.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant 12 NR_165468.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X23 XM_047443865.1:c. N/A Upstream Transcript Variant
RNASEH1 transcript variant X1 XR_007071496.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X4 XR_007071497.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X6 XR_007071498.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X7 XR_007071499.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X8 XR_007071500.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X10 XR_007071501.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X11 XR_007071502.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X12 XR_007071503.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X13 XR_007071504.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X14 XR_007071505.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X15 XR_007071506.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X16 XR_007071507.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X18 XR_007071508.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X19 XR_007071509.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X21 XR_007071510.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X22 XR_007071511.1:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X17 XR_922665.2:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X2 XR_922667.2:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X20 XR_922670.2:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X5 XR_922671.2:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X3 XR_922673.2:n. N/A Upstream Transcript Variant
RNASEH1 transcript variant X9 XR_922674.2:n. N/A Upstream Transcript Variant
Gene: RNASEH1-DT, RNASEH1 divergent transcript (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RNASEH1-DT transcript variant 2 NR_038429.1:n. N/A Intron Variant
RNASEH1-DT transcript variant 1 NR_038430.1:n. N/A Intron Variant
RNASEH1-DT transcript variant 3 NR_038431.1: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 C= T
GRCh38.p14 chr 2 NC_000002.12:g.3560005= NC_000002.12:g.3560005C>T
GRCh37.p13 chr 2 NC_000002.11:g.3607595= NC_000002.11:g.3607595C>T
RNASEH1 RefSeqGene (LRG_1090) NG_051310.1:g.3367= NG_051310.1:g.3367G>A
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, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2769138557 Nov 08, 2017 (151)
2 TOPMED ss4492365096 Apr 25, 2021 (155)
3 gnomAD - Genomes NC_000002.12 - 3560005 Apr 25, 2021 (155)
4 TopMed NC_000002.12 - 3560005 Apr 25, 2021 (155)
5 ALFA NC_000002.12 - 3560005 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
ss2769138557 NC_000002.11:3607594:C:T NC_000002.12:3560004:C:T (self)
46955245, 296187975, 6702112534, ss4492365096 NC_000002.12:3560004:C:T NC_000002.12:3560004:C:T (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 rs1486284351

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