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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.

rs542460422

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:186785632-186785634 (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
delA
Variation Type
Indel Insertion and Deletion
Frequency
delA=0.00193 (242/125568, TOPMED)
delA=0.0012 (38/31408, GnomAD)
delA=0.001 (6/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EIF4A2 : Intron Variant
MIR1248 : 2KB Upstream Variant
SNORA4 : 2KB Upstream Variant (+ 3 more)
SNORA63 : 2KB Upstream Variant
SNORA63B : 2KB Upstream Variant
SNORA81 : 2KB Upstream 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 3 NC_000003.12:g.186785634del
GRCh37.p13 chr 3 NC_000003.11:g.186503423del
Gene: EIF4A2, eukaryotic translation initiation factor 4A2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
EIF4A2 transcript NM_001967.4:c. N/A Intron Variant
Gene: SNORA63, small nucleolar RNA, H/ACA box 63 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORA63 transcript NR_002586.1:n. N/A Upstream Transcript Variant
Gene: SNORA4, small nucleolar RNA, H/ACA box 4 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORA4 transcript NR_002588.1:n. N/A Upstream Transcript Variant
Gene: SNORA81, small nucleolar RNA, H/ACA box 81 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORA81 transcript NR_002989.1:n. N/A Upstream Transcript Variant
Gene: MIR1248, microRNA 1248 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR1248 transcript NR_031650.1:n. N/A Upstream Transcript Variant
Gene: SNORA63B, small nucleolar RNA, H/ACA box 63B (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORA63B transcript NR_145766.1: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
TopMed Global Study-wide 125568 -

No frequency provided

delA=0.00193
gnomAD - Genomes Global Study-wide 31408 -

No frequency provided

delA=0.0012
gnomAD - Genomes European Sub 18906 -

No frequency provided

delA=0.0000
gnomAD - Genomes African Sub 8716 -

No frequency provided

delA=0.004
gnomAD - Genomes East Asian Sub 1560 -

No frequency provided

delA=0.000
gnomAD - Genomes Other Sub 1088 -

No frequency provided

delA=0.000
gnomAD - Genomes American Sub 848 -

No frequency provided

delA=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 -

No frequency provided

delA=0.00
1000Genomes Global Study-wide 5008 -

No frequency provided

delA=0.001
1000Genomes African Sub 1322 -

No frequency provided

delA=0.005
1000Genomes East Asian Sub 1008 -

No frequency provided

delA=0.000
1000Genomes Europe Sub 1006 -

No frequency provided

delA=0.000
1000Genomes South Asian Sub 978 -

No frequency provided

delA=0.00
1000Genomes American Sub 694 -

No frequency provided

delA=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 AAA= delA Note
GRCh38.p12 chr 3 NC_000003.12:g.18678563...

NC_000003.12:g.186785632_186785634=

NC_000003.12:g.18678563...

NC_000003.12:g.186785634del

GRCh37.p13 chr 3 NC_000003.11:g.18650342...

NC_000003.11:g.186503421_186503423=

NC_000003.11:g.18650342...

NC_000003.11:g.186503423del

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#.

4 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1371487608 Aug 21, 2014 (142)
2 GNOMAD ss2803535485 Nov 08, 2017 (151)
3 TOPMED ss3415636877 Nov 08, 2017 (151)
4 EVA_DECODE ss3711032783 Jul 13, 2019 (153)
5 1000Genomes NC_000003.11 - 186503421 Oct 12, 2018 (152)
6 gnomAD - Genomes NC_000003.11 - 186503421 Jul 13, 2019 (153)
7 TopMed NC_000003.12 - 186785632 Oct 12, 2018 (152)
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
19011597, 52046762, ss1371487608, ss2803535485 NC_000003.11:186503420:A: NC_000003.12:186785631:AAA:AA (self)
271534090, ss3415636877, ss3711032783 NC_000003.12:186785631:A: NC_000003.12:186785631:AAA:AA (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 rs542460422

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