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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.

rs1487543502

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:47483829 (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
T>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000011 (3/264690, TOPMED)
A=0.000028 (3/106537, GnomAD_exome)
A=0.000010 (1/104139, GnomAD) (+ 1 more)
A=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01560 : Non Coding Transcript Variant
ZNF41 : 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 T=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 T=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 T=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 T=1.00 A=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 T=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 T=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 T=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 T=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 T=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 T=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 T=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 466 T=1.000 A=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 T=0.999989 A=0.000011
gnomAD - Exomes Global Study-wide 106537 T=0.999972 A=0.000028
gnomAD - Exomes European Sub 52198 T=0.99994 A=0.00006
gnomAD - Exomes Asian Sub 21143 T=1.00000 A=0.00000
gnomAD - Exomes American Sub 18671 T=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 5938 T=1.0000 A=0.0000
gnomAD - Exomes African Sub 5425 T=1.0000 A=0.0000
gnomAD - Exomes Other Sub 3162 T=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 104139 T=0.999990 A=0.000010
gnomAD - Genomes European Sub 57153 T=0.99998 A=0.00002
gnomAD - Genomes African Sub 31356 T=1.00000 A=0.00000
gnomAD - Genomes American Sub 9288 T=1.0000 A=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2524 T=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 2251 T=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1567 T=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 10680 T=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 6962 T=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2294 T=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 A=0.000
Allele Frequency Aggregator Other Sub 466 T=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 108 T=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 T=1.00 A=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 X NC_000023.11:g.47483829T>A
GRCh37.p13 chr X NC_000023.10:g.47343228T>A
ZNF41 RefSeqGene NG_008238.1:g.4118A>T
Gene: ZNF41, zinc finger protein 41 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
ZNF41 transcript variant 3 NM_001324139.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 4 NM_001324140.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 5 NM_001324141.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 6 NM_001324142.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 7 NM_001324143.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 8 NM_001324144.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 9 NM_001324145.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 10 NM_001324147.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 11 NM_001324148.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 12 NM_001324149.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 13 NM_001324150.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 14 NM_001324151.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 15 NM_001324152.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 16 NM_001324153.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 1 NM_007130.4:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 2 NM_153380.3:c. N/A Upstream Transcript Variant
ZNF41 transcript variant 17 NM_001324154.1:c. N/A N/A
ZNF41 transcript variant 18 NM_001324155.1:c. N/A N/A
ZNF41 transcript variant 19 NM_001324156.1:c. N/A N/A
ZNF41 transcript variant 20 NM_001324157.1:c. N/A N/A
ZNF41 transcript variant X1 XM_006724550.4:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X9 XM_006724555.4:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X5 XM_017029810.3:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X3 XM_017029811.3:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X2 XM_017029812.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X4 XM_017029814.3:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X7 XM_017029815.2:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X10 XM_047442472.1:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X11 XM_047442473.1:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X14 XM_047442475.1:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X15 XM_047442476.1:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X16 XM_047442477.1:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X17 XM_047442478.1:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X20 XM_047442481.1:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X21 XM_047442482.1:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X23 XM_047442483.1:c. N/A Upstream Transcript Variant
ZNF41 transcript variant X6 XM_017029813.2:c. N/A N/A
ZNF41 transcript variant X13 XM_017029816.2:c. N/A N/A
ZNF41 transcript variant X22 XM_017029817.2:c. N/A N/A
ZNF41 transcript variant X8 XM_047442471.1:c. N/A N/A
ZNF41 transcript variant X12 XM_047442474.1:c. N/A N/A
ZNF41 transcript variant X18 XM_047442479.1:c. N/A N/A
ZNF41 transcript variant X19 XM_047442480.1:c. N/A N/A
ZNF41 transcript variant X24 XM_047442484.1:c. N/A N/A
Gene: LINC01560, long intergenic non-protein coding RNA 1560 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01560 transcript NR_126059.1:n.1114T>A N/A Non Coding 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 T= A
GRCh38.p14 chr X NC_000023.11:g.47483829= NC_000023.11:g.47483829T>A
GRCh37.p13 chr X NC_000023.10:g.47343228= NC_000023.10:g.47343228T>A
ZNF41 RefSeqGene NG_008238.1:g.4118= NG_008238.1:g.4118A>T
LINC01560 transcript NR_126059.1:n.1114= NR_126059.1:n.1114T>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#.

3 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2745377959 Nov 08, 2017 (151)
2 GNOMAD ss4371035836 Apr 27, 2021 (155)
3 TOPMED ss5121987485 Apr 27, 2021 (155)
4 gnomAD - Genomes NC_000023.11 - 47483829 Apr 27, 2021 (155)
5 gnomAD - Exomes NC_000023.10 - 47343228 Jul 13, 2019 (153)
6 TopMed NC_000023.11 - 47483829 Apr 27, 2021 (155)
7 ALFA NC_000023.11 - 47483829 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
14713377, ss2745377959 NC_000023.10:47343227:T:A NC_000023.11:47483828:T:A (self)
580052649, 685593842, 4384894357, ss4371035836, ss5121987485 NC_000023.11:47483828:T:A NC_000023.11:47483828:T:A (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 rs1487543502

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