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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.

rs760355583

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:49121511 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/251432, GnomAD_exome)
A=0.000016 (2/121288, ExAC)
A=0.000 (0/478, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LAMB2 : Stop Gained
USP19 : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 478 G=1.000 A=0.000
European Sub 0 G=0 A=0
African Sub 426 G=1.000 A=0.000
African Others Sub 0 G=0 A=0
African American Sub 426 G=1.000 A=0.000
Asian Sub 0 G=0 A=0
East Asian Sub 0 G=0 A=0
Other Asian Sub 0 G=0 A=0
Latin American 1 Sub 0 G=0 A=0
Latin American 2 Sub 0 G=0 A=0
South Asian Sub 0 G=0 A=0
Other Sub 52 G=1.00 A=0.00


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 251432 G=0.999996 A=0.000004
gnomAD - Exomes European Sub 135362 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 49010 G=0.99998 A=0.00002
gnomAD - Exomes American Sub 34588 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16256 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6138 G=1.0000 A=0.0000
ExAC Global Study-wide 121288 G=0.999984 A=0.000016
ExAC Europe Sub 73252 G=1.00000 A=0.00000
ExAC Asian Sub 25166 G=0.99992 A=0.00008
ExAC American Sub 11568 G=1.00000 A=0.00000
ExAC African Sub 10396 G=1.00000 A=0.00000
ExAC Other Sub 906 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 478 G=1.000 A=0.000
Allele Frequency Aggregator African Sub 426 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 52 G=1.00 A=0.00
Allele Frequency Aggregator European Sub 0 G=0 A=0
Allele Frequency Aggregator Latin American 1 Sub 0 G=0 A=0
Allele Frequency Aggregator Latin American 2 Sub 0 G=0 A=0
Allele Frequency Aggregator South Asian Sub 0 G=0 A=0
Allele Frequency Aggregator Asian Sub 0 G=0 A=0
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 3 NC_000003.12:g.49121511G>A
GRCh37.p13 chr 3 NC_000003.11:g.49158944G>A
USP19 RefSeqGene NG_054716.1:g.4428C>T
LAMB2 RefSeqGene NG_008094.1:g.16656C>T
Gene: USP19, ubiquitin specific peptidase 19 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
USP19 transcript variant 1 NM_001199160.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 2 NM_001199161.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 3 NM_001199162.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 5 NM_001351098.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 6 NM_001351099.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 7 NM_001351100.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 8 NM_001351101.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 9 NM_001351102.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 10 NM_001351103.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 11 NM_001351104.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 12 NM_001351105.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 13 NM_001351106.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 14 NM_001351107.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 15 NM_001351108.2:c. N/A Upstream Transcript Variant
USP19 transcript variant 16 NM_001389594.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 17 NM_001389595.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 18 NM_001389596.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 19 NM_001389597.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 20 NM_001389598.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 21 NM_001389599.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 22 NM_001389600.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 23 NM_001389601.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 24 NM_001389602.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 25 NM_001389603.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 26 NM_001389604.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 27 NM_001389605.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 28 NM_001389606.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 29 NM_001389607.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 30 NM_001389608.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 31 NM_001400288.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 32 NM_001400290.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 33 NM_001400292.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 34 NM_001400293.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 35 NM_001400294.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 36 NM_001400295.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 37 NM_001400296.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 38 NM_001400297.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 39 NM_001400298.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 40 NM_001400299.1:c. N/A Upstream Transcript Variant
USP19 transcript variant 4 NM_006677.3:c. N/A Upstream Transcript Variant
USP19 transcript variant X1 XM_005264823.4:c. N/A Upstream Transcript Variant
USP19 transcript variant X2 XM_005264824.3:c. N/A Upstream Transcript Variant
USP19 transcript variant X5 XM_005264827.3:c. N/A Upstream Transcript Variant
USP19 transcript variant X3 XM_006712946.4:c. N/A Upstream Transcript Variant
USP19 transcript variant X8 XM_006712947.3:c. N/A Upstream Transcript Variant
USP19 transcript variant X15 XM_017005627.2:c. N/A Upstream Transcript Variant
USP19 transcript variant X4 XM_047447341.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X6 XM_047447342.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X7 XM_047447343.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X9 XM_047447344.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X10 XM_047447345.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X11 XM_047447346.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X12 XM_047447347.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X13 XM_047447348.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X14 XM_047447349.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X16 XM_047447350.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X17 XM_047447351.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X18 XM_047447352.1:c. N/A Upstream Transcript Variant
USP19 transcript variant X19 XM_047447353.1:c. N/A Upstream Transcript Variant
Gene: LAMB2, laminin subunit beta 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LAMB2 transcript NM_002292.4:c.5182C>T Q [CAG] > * [TAG] Coding Sequence Variant
laminin subunit beta-2 precursor NP_002283.3:p.Gln1728Ter Q (Gln) > * (Ter) Stop Gained
LAMB2 transcript variant X1 XM_005265127.5:c.5182C>T Q [CAG] > * [TAG] Coding Sequence Variant
laminin subunit beta-2 isoform X1 XP_005265184.1:p.Gln1728T…

XP_005265184.1:p.Gln1728Ter

 		Q (Gln) > * (Ter) Stop Gained
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
GRCh38.p14 chr 3 NC_000003.12:g.49121511= NC_000003.12:g.49121511G>A
GRCh37.p13 chr 3 NC_000003.11:g.49158944= NC_000003.11:g.49158944G>A
USP19 RefSeqGene NG_054716.1:g.4428= NG_054716.1:g.4428C>T
LAMB2 RefSeqGene NG_008094.1:g.16656= NG_008094.1:g.16656C>T
LAMB2 transcript NM_002292.4:c.5182= NM_002292.4:c.5182C>T
LAMB2 transcript NM_002292.3:c.5182= NM_002292.3:c.5182C>T
LAMB2 transcript variant X1 XM_005265127.5:c.5182= XM_005265127.5:c.5182C>T
LAMB2 transcript variant X1 XM_005265127.4:c.5182= XM_005265127.4:c.5182C>T
LAMB2 transcript variant X1 XM_005265127.3:c.5182= XM_005265127.3:c.5182C>T
LAMB2 transcript variant X1 XM_005265127.2:c.5182= XM_005265127.2:c.5182C>T
LAMB2 transcript variant X1 XM_005265127.1:c.5182= XM_005265127.1:c.5182C>T
laminin subunit beta-2 precursor NP_002283.3:p.Gln1728= NP_002283.3:p.Gln1728Ter
laminin subunit beta-2 isoform X1 XP_005265184.1:p.Gln1728= XP_005265184.1:p.Gln1728Ter
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#.

6 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1687003331 Apr 01, 2015 (144)
2 GNOMAD ss2733748130 Nov 08, 2017 (151)
3 ILLUMINA ss3022237846 Nov 08, 2017 (151)
4 ILLUMINA ss3652709628 Oct 12, 2018 (152)
5 ILLUMINA ss3726014068 Jul 13, 2019 (153)
6 EVA ss5339626148 Oct 12, 2022 (156)
7 ExAC NC_000003.11 - 49158944 Oct 12, 2018 (152)
8 gnomAD - Exomes NC_000003.11 - 49158944 Jul 13, 2019 (153)
9 ALFA NC_000003.12 - 49121511 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
6927419, 2826579, ss1687003331, ss2733748130, ss3022237846, ss3652709628, ss5339626148 NC_000003.11:49158943:G:A NC_000003.12:49121510:G:A (self)
2168457494, ss3726014068 NC_000003.12:49121510:G:A NC_000003.12:49121510:G: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 rs760355583

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.post761+d5e8e07