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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.

rs1470875739

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:230402820 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
A=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SP140L : Missense Variant
LOC105373925 : 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 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 G=1.00 A=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 466 G=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 G=0.999996 A=0.000004
Allele Frequency Aggregator Total Global 10680 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 6962 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2294 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 466 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 G=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 2 NC_000002.12:g.230402820G>A
GRCh38.p14 chr 2 NC_000002.12:g.230402820G>T
GRCh37.p13 chr 2 NC_000002.11:g.231267535G>A
GRCh37.p13 chr 2 NC_000002.11:g.231267535G>T
Gene: SP140L, SP140 nuclear body protein like (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SP140L transcript variant 1 NM_138402.6:c.1667G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 1 NP_612411.4:p.Gly556Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant 1 NM_138402.6:c.1667G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 1 NP_612411.4:p.Gly556Val G (Gly) > V (Val) Missense Variant
SP140L transcript variant 4 NM_001352892.2:c.1640G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 4 NP_001339821.1:p.Gly547Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant 4 NM_001352892.2:c.1640G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 4 NP_001339821.1:p.Gly547Val G (Gly) > V (Val) Missense Variant
SP140L transcript variant 6 NM_001352894.2:c.1460G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 6 NP_001339823.1:p.Gly487Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant 6 NM_001352894.2:c.1460G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 6 NP_001339823.1:p.Gly487Val G (Gly) > V (Val) Missense Variant
SP140L transcript variant 5 NM_001352893.2:c.1562G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 5 NP_001339822.1:p.Gly521Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant 5 NM_001352893.2:c.1562G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 5 NP_001339822.1:p.Gly521Val G (Gly) > V (Val) Missense Variant
SP140L transcript variant 3 NM_001308163.3:c.1487G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 3 NP_001295092.1:p.Gly496Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant 3 NM_001308163.3:c.1487G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 3 NP_001295092.1:p.Gly496Val G (Gly) > V (Val) Missense Variant
SP140L transcript variant 2 NM_001308162.3:c.1592G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 2 NP_001295091.1:p.Gly531Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant 2 NM_001308162.3:c.1592G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform 2 NP_001295091.1:p.Gly531Val G (Gly) > V (Val) Missense Variant
SP140L transcript variant 7 NR_148198.2:n.1617G>A N/A Non Coding Transcript Variant
SP140L transcript variant 7 NR_148198.2:n.1617G>T N/A Non Coding Transcript Variant
SP140L transcript variant X8 XM_011512190.4:c. N/A Genic Downstream Transcript Variant
SP140L transcript variant X13 XM_011512191.2:c. N/A Genic Downstream Transcript Variant
SP140L transcript variant X12 XM_017005301.3:c. N/A Genic Downstream Transcript Variant
SP140L transcript variant X7 XM_047446417.1:c. N/A Genic Downstream Transcript Variant
SP140L transcript variant X9 XM_047446418.1:c. N/A Genic Downstream Transcript Variant
SP140L transcript variant X10 XM_047446419.1:c. N/A Genic Downstream Transcript Variant
SP140L transcript variant X11 XM_047446420.1:c. N/A Genic Downstream Transcript Variant
SP140L transcript variant X14 XM_047446421.1:c. N/A Genic Downstream Transcript Variant
SP140L transcript variant X5 XM_006712856.2:c.1535G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X5 XP_006712919.1:p.Gly512Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant X5 XM_006712856.2:c.1535G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X5 XP_006712919.1:p.Gly512Val G (Gly) > V (Val) Missense Variant
SP140L transcript variant X1 XM_047446412.1:c.1691G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X1 XP_047302368.1:p.Gly564Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant X1 XM_047446412.1:c.1691G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X1 XP_047302368.1:p.Gly564Val G (Gly) > V (Val) Missense Variant
SP140L transcript variant X2 XM_047446413.1:c.1613G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X2 XP_047302369.1:p.Gly538Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant X2 XM_047446413.1:c.1613G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X2 XP_047302369.1:p.Gly538Val G (Gly) > V (Val) Missense Variant
SP140L transcript variant X3 XM_047446414.1:c.1565G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X3 XP_047302370.1:p.Gly522Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant X3 XM_047446414.1:c.1565G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X3 XP_047302370.1:p.Gly522Val G (Gly) > V (Val) Missense Variant
SP140L transcript variant X4 XM_047446415.1:c.1538G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X4 XP_047302371.1:p.Gly513Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant X4 XM_047446415.1:c.1538G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X4 XP_047302371.1:p.Gly513Val G (Gly) > V (Val) Missense Variant
SP140L transcript variant X6 XM_047446416.1:c.1511G>A G [GGA] > E [GAA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X6 XP_047302372.1:p.Gly504Glu G (Gly) > E (Glu) Missense Variant
SP140L transcript variant X6 XM_047446416.1:c.1511G>T G [GGA] > V [GTA] Coding Sequence Variant
nuclear body protein SP140-like protein isoform X6 XP_047302372.1:p.Gly504Val G (Gly) > V (Val) Missense Variant
Gene: LOC105373925, uncharacterized LOC105373925 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC105373925 transcript variant X1 XR_001739921.2:n. N/A Upstream Transcript Variant
LOC105373925 transcript variant X2 XR_001739922.2:n. N/A Upstream Transcript Variant
LOC105373925 transcript variant X3 XR_001739924.2: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

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 T
GRCh38.p14 chr 2 NC_000002.12:g.230402820= NC_000002.12:g.230402820G>A NC_000002.12:g.230402820G>T
GRCh37.p13 chr 2 NC_000002.11:g.231267535= NC_000002.11:g.231267535G>A NC_000002.11:g.231267535G>T
SP140L transcript variant 1 NM_138402.6:c.1667= NM_138402.6:c.1667G>A NM_138402.6:c.1667G>T
SP140L transcript variant 1 NM_138402.5:c.1667= NM_138402.5:c.1667G>A NM_138402.5:c.1667G>T
SP140L transcript variant 1 NM_138402.4:c.1667= NM_138402.4:c.1667G>A NM_138402.4:c.1667G>T
SP140L transcript variant 2 NM_001308162.3:c.1592= NM_001308162.3:c.1592G>A NM_001308162.3:c.1592G>T
SP140L transcript variant 2 NM_001308162.2:c.1592= NM_001308162.2:c.1592G>A NM_001308162.2:c.1592G>T
SP140L transcript variant 2 NM_001308162.1:c.1592= NM_001308162.1:c.1592G>A NM_001308162.1:c.1592G>T
SP140L transcript variant 3 NM_001308163.3:c.1487= NM_001308163.3:c.1487G>A NM_001308163.3:c.1487G>T
SP140L transcript variant 3 NM_001308163.2:c.1487= NM_001308163.2:c.1487G>A NM_001308163.2:c.1487G>T
SP140L transcript variant 3 NM_001308163.1:c.1487= NM_001308163.1:c.1487G>A NM_001308163.1:c.1487G>T
SP140L transcript variant 4 NM_001352892.2:c.1640= NM_001352892.2:c.1640G>A NM_001352892.2:c.1640G>T
SP140L transcript variant 4 NM_001352892.1:c.1640= NM_001352892.1:c.1640G>A NM_001352892.1:c.1640G>T
SP140L transcript variant 5 NM_001352893.2:c.1562= NM_001352893.2:c.1562G>A NM_001352893.2:c.1562G>T
SP140L transcript variant 5 NM_001352893.1:c.1562= NM_001352893.1:c.1562G>A NM_001352893.1:c.1562G>T
SP140L transcript variant 7 NR_148198.2:n.1617= NR_148198.2:n.1617G>A NR_148198.2:n.1617G>T
SP140L transcript variant 7 NR_148198.1:n.1639= NR_148198.1:n.1639G>A NR_148198.1:n.1639G>T
SP140L transcript variant X5 XM_006712856.2:c.1535= XM_006712856.2:c.1535G>A XM_006712856.2:c.1535G>T
SP140L transcript variant X8 XM_006712856.1:c.1535= XM_006712856.1:c.1535G>A XM_006712856.1:c.1535G>T
SP140L transcript variant 6 NM_001352894.2:c.1460= NM_001352894.2:c.1460G>A NM_001352894.2:c.1460G>T
SP140L transcript variant 6 NM_001352894.1:c.1460= NM_001352894.1:c.1460G>A NM_001352894.1:c.1460G>T
SP140L transcript variant X1 XM_047446412.1:c.1691= XM_047446412.1:c.1691G>A XM_047446412.1:c.1691G>T
SP140L transcript variant X2 XM_047446413.1:c.1613= XM_047446413.1:c.1613G>A XM_047446413.1:c.1613G>T
SP140L transcript variant X3 XM_047446414.1:c.1565= XM_047446414.1:c.1565G>A XM_047446414.1:c.1565G>T
SP140L transcript variant X4 XM_047446415.1:c.1538= XM_047446415.1:c.1538G>A XM_047446415.1:c.1538G>T
SP140L transcript variant X6 XM_047446416.1:c.1511= XM_047446416.1:c.1511G>A XM_047446416.1:c.1511G>T
nuclear body protein SP140-like protein isoform 1 NP_612411.4:p.Gly556= NP_612411.4:p.Gly556Glu NP_612411.4:p.Gly556Val
nuclear body protein SP140-like protein isoform 2 NP_001295091.1:p.Gly531= NP_001295091.1:p.Gly531Glu NP_001295091.1:p.Gly531Val
nuclear body protein SP140-like protein isoform 3 NP_001295092.1:p.Gly496= NP_001295092.1:p.Gly496Glu NP_001295092.1:p.Gly496Val
nuclear body protein SP140-like protein isoform 4 NP_001339821.1:p.Gly547= NP_001339821.1:p.Gly547Glu NP_001339821.1:p.Gly547Val
nuclear body protein SP140-like protein isoform 5 NP_001339822.1:p.Gly521= NP_001339822.1:p.Gly521Glu NP_001339822.1:p.Gly521Val
nuclear body protein SP140-like protein isoform X5 XP_006712919.1:p.Gly512= XP_006712919.1:p.Gly512Glu XP_006712919.1:p.Gly512Val
nuclear body protein SP140-like protein isoform 6 NP_001339823.1:p.Gly487= NP_001339823.1:p.Gly487Glu NP_001339823.1:p.Gly487Val
nuclear body protein SP140-like protein isoform X1 XP_047302368.1:p.Gly564= XP_047302368.1:p.Gly564Glu XP_047302368.1:p.Gly564Val
nuclear body protein SP140-like protein isoform X2 XP_047302369.1:p.Gly538= XP_047302369.1:p.Gly538Glu XP_047302369.1:p.Gly538Val
nuclear body protein SP140-like protein isoform X3 XP_047302370.1:p.Gly522= XP_047302370.1:p.Gly522Glu XP_047302370.1:p.Gly522Val
nuclear body protein SP140-like protein isoform X4 XP_047302371.1:p.Gly513= XP_047302371.1:p.Gly513Glu XP_047302371.1:p.Gly513Val
nuclear body protein SP140-like protein isoform X6 XP_047302372.1:p.Gly504= XP_047302372.1:p.Gly504Glu XP_047302372.1:p.Gly504Val
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 GNOMAD ss2733398167 Nov 08, 2017 (151)
2 TOPMED ss4548011081 Apr 27, 2021 (155)
3 TopMed NC_000002.12 - 230402820 Apr 27, 2021 (155)
4 ALFA NC_000002.12 - 230402820 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
351833960, 13529454380, ss4548011081 NC_000002.12:230402819:G:A NC_000002.12:230402819:G:A (self)
ss2733398167 NC_000002.11:231267534:G:T NC_000002.12:230402819:G:T (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 rs1470875739

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