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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 Aliases 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.

rs746509971

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr1:173865657 (GRCh38.p12) 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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00000 (1/232086, GnomAD_exome)
G=0.00001 (1/112776, ExAC)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SNORD78 : Non Coding Transcript Variant
GAS5 : Intron Variant
SNORD47 : 2KB Upstream Variant (+ 4 more)
SNORD79 : 2KB Upstream Variant
SNORD80 : 2KB Upstream Variant
SNORD81 : 2KB Upstream Variant
SNORD44 : 500B Downstream Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 1 NC_000001.11:g.173865657A>G
GRCh37.p13 chr 1 NC_000001.10:g.173834795A>G
Gene: SNORD78, small nucleolar RNA, C/D box 78 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SNORD78 transcript NR_003944.2:n.30T>C N/A Non Coding Transcript Variant
Gene: GAS5, growth arrest specific 5 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GAS5 transcript variant 1 NR_002578.3:n. N/A Intron Variant
GAS5 transcript variant 2 NR_152521.1:n. N/A Intron Variant
GAS5 transcript variant 3 NR_152522.1:n. N/A Intron Variant
GAS5 transcript variant 4 NR_152523.1:n. N/A Intron Variant
GAS5 transcript variant 5 NR_152524.1:n. N/A Intron Variant
GAS5 transcript variant 6 NR_152525.1:n. N/A Intron Variant
GAS5 transcript variant 7 NR_152526.1:n. N/A Intron Variant
GAS5 transcript variant 8 NR_152527.1:n. N/A Intron Variant
GAS5 transcript variant 9 NR_152528.1:n. N/A Intron Variant
GAS5 transcript variant 10 NR_152529.1:n. N/A Intron Variant
GAS5 transcript variant 11 NR_152530.1:n. N/A Intron Variant
GAS5 transcript variant 12 NR_152531.1:n. N/A Intron Variant
GAS5 transcript variant 13 NR_152532.1:n. N/A Intron Variant
GAS5 transcript variant 14 NR_152533.1:n. N/A Intron Variant
GAS5 transcript variant 15 NR_152534.1:n. N/A Intron Variant
Gene: SNORD47, small nucleolar RNA, C/D box 47 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORD47 transcript NR_002746.1:n. N/A Upstream Transcript Variant
Gene: SNORD44, small nucleolar RNA, C/D box 44 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORD44 transcript NR_002750.2:n. N/A Downstream Transcript Variant
Gene: SNORD81, small nucleolar RNA, C/D box 81 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORD81 transcript NR_003938.2:n. N/A Upstream Transcript Variant
Gene: SNORD79, small nucleolar RNA, C/D box 79 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORD79 transcript NR_003939.1:n. N/A Upstream Transcript Variant
Gene: SNORD80, small nucleolar RNA, C/D box 80 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORD80 transcript NR_003940.1: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

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 - Exomes Global Study-wide 232086 A=1.00000 G=0.00000
gnomAD - Exomes European Sub 120182 A=1.00000 G=0.00000
gnomAD - Exomes Asian Sub 47898 A=1.0000 G=0.0000
gnomAD - Exomes American Sub 34312 A=1.0000 G=0.0000
gnomAD - Exomes African Sub 13956 A=1.0000 G=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 9860 A=1.000 G=0.000
gnomAD - Exomes Other Sub 5878 A=1.000 G=0.000
ExAC Global Study-wide 112776 A=0.99999 G=0.00001
ExAC Europe Sub 68010 A=1.0000 G=0.0000
ExAC Asian Sub 24418 A=1.0000 G=0.0000
ExAC American Sub 11354 A=1.0000 G=0.0000
ExAC African Sub 8152 A=1.000 G=0.000
ExAC Other Sub 842 A=1.00 G=0.00
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 A= G Note
GRCh38.p12 chr 1 NC_000001.11:g.173865657= NC_000001.11:g.17386565...

NC_000001.11:g.173865657A>G

GRCh37.p13 chr 1 NC_000001.10:g.173834795= NC_000001.10:g.17383479...

NC_000001.10:g.173834795A>G

SNORD78 transcript NR_003944.2:n.30= NR_003944.2:n.30T>C
SNORD78 transcript NR_003944.1:n.30= NR_003944.1:n.30T>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 EVA_EXAC ss1685918862 Apr 01, 2015 (144)
2 GNOMAD ss2732066483 Nov 08, 2017 (151)
3 ExAC NC_000001.10 - 173834795 Oct 11, 2018 (152)
4 gnomAD - Exomes NC_000001.10 - 173834795 Jul 12, 2019 (153)
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
5145473, 1095650, ss1685918862, ss2732066483 NC_000001.10:173834794:A:G NC_000001.11:173865656:A:G (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 rs746509971

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.post308+0fe9b3b