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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs1057519880

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr19:49665875 (GRCh38.p7) 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=0.00000 (1/245828, GnomAD)
Clinical Significance
Reported in ClinVar
Gene : Consequence
BCL2L12 : Missense Variant
IRF3 : Non Coding Transcript Variant
Publications
1 citation
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.p7 chr 19 NC_000019.10:g.49665875C>T
GRCh37.p13 chr 19 NC_000019.9:g.50169132C>T
IRF3 RefSeqGene NG_031810.1:g.5001G>A
Gene: IRF3, interferon regulatory factor 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IRF3 transcript variant 1 NM_001571.5:c. N/A 5 Prime UTR Variant
IRF3 transcript variant 2 NM_001197122.1:c. N/A 5 Prime UTR Variant
IRF3 transcript variant 3 NM_001197123.1:c. N/A 5 Prime UTR Variant
IRF3 transcript variant 4 NM_001197124.1:c. N/A 5 Prime UTR Variant
IRF3 transcript variant 6 NM_001197126.1:c. N/A 5 Prime UTR Variant
IRF3 transcript variant 5 NM_001197125.1:c. N/A 5 Prime UTR Variant
IRF3 transcript variant 7 NM_001197127.1:c. N/A 5 Prime UTR Variant
IRF3 transcript variant 8 NM_001197128.1:c. N/A 5 Prime UTR Variant
IRF3 transcript variant 9 NR_045568.1:n.1G>A N/A Non Coding Transcript Variant
IRF3 transcript variant X3 XM_006723197.1:c. N/A Genic Upstream Transcript Variant
IRF3 transcript variant X2 XM_006723198.1:c. N/A Genic Upstream Transcript Variant
IRF3 transcript variant X7 XM_006723200.1:c. N/A Genic Upstream Transcript Variant
IRF3 transcript variant X14 XM_006723201.1:c. N/A Genic Upstream Transcript Variant
IRF3 transcript variant X9 XM_006723202.2:c. N/A Genic Upstream Transcript Variant
IRF3 transcript variant X3 XM_017026766.1:c. N/A Genic Upstream Transcript Variant
IRF3 transcript variant X4 XM_017026767.1:c. N/A Genic Upstream Transcript Variant
IRF3 transcript variant X6 XR_001753677.1:n. N/A Genic Upstream Transcript Variant
IRF3 transcript variant X10 XR_001753678.1:n. N/A Genic Upstream Transcript Variant
Gene: BCL2L12, BCL2 like 12 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BCL2L12 transcript variant 1 NM_138639.1:c.52C>T R [CGG] > W [TGG] Coding Sequence Variant
bcl-2-like protein 12 isoform 1 NP_619580.1:p.Arg...

NP_619580.1:p.Arg18Trp

R (Arg) > W (Trp) Missense Variant
BCL2L12 transcript variant 3 NM_001040668.1:c....

NM_001040668.1:c.52C>T

R [CGG] > W [TGG] Coding Sequence Variant
bcl-2-like protein 12 isoform 3 NP_001035758.1:p....

NP_001035758.1:p.Arg18Trp

R (Arg) > W (Trp) Missense Variant
BCL2L12 transcript variant 4 NM_001282516.1:c....

NM_001282516.1:c.52C>T

R [CGG] > W [TGG] Coding Sequence Variant
bcl-2-like protein 12 isoform 4 NP_001269445.1:p....

NP_001269445.1:p.Arg18Trp

R (Arg) > W (Trp) Missense Variant
BCL2L12 transcript variant 5 NM_001282517.1:c....

NM_001282517.1:c.52C>T

R [CGG] > W [TGG] Coding Sequence Variant
bcl-2-like protein 12 isoform 2 NP_001269446.1:p....

NP_001269446.1:p.Arg18Trp

R (Arg) > W (Trp) Missense Variant
BCL2L12 transcript variant 8 NM_001282519.1:c....

NM_001282519.1:c.52C>T

R [CGG] > W [TGG] Coding Sequence Variant
bcl-2-like protein 12 isoform 5 NP_001269448.1:p....

NP_001269448.1:p.Arg18Trp

R (Arg) > W (Trp) Missense Variant
BCL2L12 transcript variant 10 NM_001282520.1:c....

NM_001282520.1:c.52C>T

R [CGG] > W [TGG] Coding Sequence Variant
bcl-2-like protein 12 isoform 6 NP_001269449.1:p....

NP_001269449.1:p.Arg18Trp

R (Arg) > W (Trp) Missense Variant
BCL2L12 transcript variant 12 NM_001282521.1:c....

NM_001282521.1:c.52C>T

R [CGG] > W [TGG] Coding Sequence Variant
bcl-2-like protein 12 isoform 7 NP_001269450.1:p....

NP_001269450.1:p.Arg18Trp

R (Arg) > W (Trp) Missense Variant
BCL2L12 transcript variant 2 NR_104200.1:n.734C>T N/A Non Coding Transcript Variant
BCL2L12 transcript variant 6 NR_104201.1:n.734C>T N/A Non Coding Transcript Variant
BCL2L12 transcript variant 7 NR_104202.1:n.734C>T N/A Non Coding Transcript Variant
BCL2L12 transcript variant 9 NR_104203.1:n.734C>T N/A Non Coding Transcript Variant
BCL2L12 transcript variant 11 NR_104204.1:n.734C>T N/A Non Coding Transcript Variant
BCL2L12 transcript variant 13 NR_104205.1:n.734C>T N/A Non Coding Transcript Variant
BCL2L12 transcript variant X1 XM_017027345.1:c....

XM_017027345.1:c.52C>T

R [CGG] > W [TGG] Coding Sequence Variant
bcl-2-like protein 12 isoform X1 XP_016882834.1:p....

XP_016882834.1:p.Arg18Trp

R (Arg) > W (Trp) Missense Variant
BCL2L12 transcript variant X2 XM_017027346.1:c....

XM_017027346.1:c.52C>T

R [CGG] > W [TGG] Coding Sequence Variant
bcl-2-like protein 12 isoform X2 XP_016882835.1:p....

XP_016882835.1:p.Arg18Trp

R (Arg) > W (Trp) Missense 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.

Allele: T (allele ID: 363252 )
ClinVar Accession Disease Names Clinical Significance
RCV000426971.1 Malignant melanoma of skin Likely-Pathogenic
RCV000442298.1 Squamous cell carcinoma of the skin Likely-Pathogenic
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
The Genome Aggregation Database Global Study-wide 245828 C=1.00000 T=0.00000
The Genome Aggregation Database European Sub 133702 C=1.00000 T=0.00000
The Genome Aggregation Database Asian Sub 48008 C=1.0000 T=0.0000
The Genome Aggregation Database American Sub 33574 C=1.0000 T=0.0000
The Genome Aggregation Database African Sub 15234 C=1.0000 T=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9826 C=1.000 T=0.000
The Genome Aggregation Database Other Sub 5484 C=1.000 T=0.000
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 Note
GRCh38.p7 chr 19 NC_000019.10:g.49665875C= NC_000019.10:g.49665875C>T
GRCh37.p13 chr 19 NC_000019.9:g.50169132C= NC_000019.9:g.50169132C>T
IRF3 RefSeqGene NG_031810.1:g.5001G= NG_031810.1:g.5001G>A
IRF3 transcript variant 1 NM_001571.5:c.-253G= NM_001571.5:c.-253G>A
IRF3 transcript variant 9 NR_045568.1:n.1G= NR_045568.1:n.1G>A
IRF3 transcript variant 3 NM_001197123.1:c.-416G= NM_001197123.1:c.-416G>A
IRF3 transcript variant 2 NM_001197122.1:c.-253G= NM_001197122.1:c.-253G>A
IRF3 transcript variant 5 NM_001197125.1:c.-518G= NM_001197125.1:c.-518G>A
IRF3 transcript variant 6 NM_001197126.1:c.-346G= NM_001197126.1:c.-346G>A
IRF3 transcript variant 4 NM_001197124.1:c.-253G= NM_001197124.1:c.-253G>A
IRF3 transcript variant 7 NM_001197127.1:c.-518G= NM_001197127.1:c.-518G>A
IRF3 transcript variant 8 NM_001197128.1:c.-346G= NM_001197128.1:c.-346G>A
BCL2L12 transcript variant X2 XM_017027346.1:c.52C= XM_017027346.1:c.52C>T
BCL2L12 transcript variant 6 NR_104201.1:n.734C= NR_104201.1:n.734C>T
BCL2L12 transcript variant 1 NM_138639.1:c.52C= NM_138639.1:c.52C>T
BCL2L12 transcript variant 3 NM_001040668.1:c.52C= NM_001040668.1:c.52C>T
BCL2L12 transcript variant 7 NR_104202.1:n.734C= NR_104202.1:n.734C>T
BCL2L12 transcript variant 2 NR_104200.1:n.734C= NR_104200.1:n.734C>T
BCL2L12 transcript variant X1 XM_017027345.1:c.52C= XM_017027345.1:c.52C>T
BCL2L12 transcript variant 8 NM_001282519.1:c.52C= NM_001282519.1:c.52C>T
BCL2L12 transcript variant 4 NM_001282516.1:c.52C= NM_001282516.1:c.52C>T
BCL2L12 transcript variant 10 NM_001282520.1:c.52C= NM_001282520.1:c.52C>T
BCL2L12 transcript variant 9 NR_104203.1:n.734C= NR_104203.1:n.734C>T
BCL2L12 transcript variant 5 NM_001282517.1:c.52C= NM_001282517.1:c.52C>T
BCL2L12 transcript variant 12 NM_001282521.1:c.52C= NM_001282521.1:c.52C>T
BCL2L12 transcript variant 11 NR_104204.1:n.734C= NR_104204.1:n.734C>T
BCL2L12 transcript variant 13 NR_104205.1:n.734C= NR_104205.1:n.734C>T
bcl-2-like protein 12 isoform X2 XP_016882835.1:p.Arg18= XP_016882835.1:p.Arg18Trp
bcl-2-like protein 12 isoform 1 NP_619580.1:p.Arg18= NP_619580.1:p.Arg18Trp
bcl-2-like protein 12 isoform 3 NP_001035758.1:p.Arg18= NP_001035758.1:p.Arg18Trp
bcl-2-like protein 12 isoform X1 XP_016882834.1:p.Arg18= XP_016882834.1:p.Arg18Trp
bcl-2-like protein 12 isoform 5 NP_001269448.1:p.Arg18= NP_001269448.1:p.Arg18Trp
bcl-2-like protein 12 isoform 4 NP_001269445.1:p.Arg18= NP_001269445.1:p.Arg18Trp
bcl-2-like protein 12 isoform 6 NP_001269449.1:p.Arg18= NP_001269449.1:p.Arg18Trp
bcl-2-like protein 12 isoform 2 NP_001269446.1:p.Arg18= NP_001269446.1:p.Arg18Trp
bcl-2-like protein 12 isoform 7 NP_001269450.1:p.Arg18= NP_001269450.1:p.Arg18Trp
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 ClinVar, 3 SubSNP, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss2137498196 Apr 13, 2017 (150)
2 CLINVAR ss2137504593 Apr 18, 2017 (150)
3 GNOMAD ss2744202854 Nov 08, 2017 (151)
4 The Genome Aggregation Database NC_000019.9 - 50169132 Jul 20, 2018 (151)
5 ClinVar RCV000426971.1 Jul 20, 2018 (151)
6 ClinVar RCV000442298.1 Jul 20, 2018 (151)
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
13217589, ss2744202854 NC_000019.9:50169131:C= NC_000019.10:49665874:C= (self)
ss2137498196, ss2137504593 NC_000019.10:49665874:C= NC_000019.10:49665874:C= (self)
13217589, ss2744202854 NC_000019.9:50169131:C>T NC_000019.10:49665874:C>T (self)
RCV000426971.1, RCV000442298.1, ss2137498196, ss2137504593 NC_000019.10:49665874:C>T NC_000019.10:49665874: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.

1 citation for rs1057519880
PMID Title Author Year Journal
26619011 Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Chang MT et al. 2016 Nature biotechnology

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: 0.1.4.post833+d3ba21e