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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.

rs1490115279

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:130139608 (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
T=0.000004 (1/249580, GnomAD_exome)
T=0.0001 (1/8988, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CCDC74B : Stop Gained
MED15P9 : 500B Downstream 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 8988 G=0.9999 T=0.0001 0.999777 0.0 0.000223 0
European Sub 6062 G=0.9998 T=0.0002 0.99967 0.0 0.00033 0
African Sub 594 G=1.000 T=0.000 1.0 0.0 0.0 N/A
African Others Sub 8 G=1.0 T=0.0 1.0 0.0 0.0 N/A
African American Sub 586 G=1.000 T=0.000 1.0 0.0 0.0 N/A
Asian Sub 56 G=1.00 T=0.00 1.0 0.0 0.0 N/A
East Asian Sub 26 G=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 30 G=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 0 G=0 T=0 0 0 0 N/A
Latin American 2 Sub 0 G=0 T=0 0 0 0 N/A
South Asian Sub 0 G=0 T=0 0 0 0 N/A
Other Sub 2276 G=1.0000 T=0.0000 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
gnomAD - Exomes Global Study-wide 249580 G=0.999996 T=0.000004
gnomAD - Exomes European Sub 134108 G=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48866 G=1.00000 T=0.00000
gnomAD - Exomes American Sub 34484 G=1.00000 T=0.00000
gnomAD - Exomes African Sub 16014 G=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10020 G=0.99990 T=0.00010
gnomAD - Exomes Other Sub 6088 G=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 8988 G=0.9999 T=0.0001
Allele Frequency Aggregator European Sub 6062 G=0.9998 T=0.0002
Allele Frequency Aggregator Other Sub 2276 G=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 594 G=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 56 G=1.00 T=0.00
Allele Frequency Aggregator Latin American 1 Sub 0 G=0 T=0
Allele Frequency Aggregator Latin American 2 Sub 0 G=0 T=0
Allele Frequency Aggregator South Asian Sub 0 G=0 T=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 2 NC_000002.12:g.130139608G>A
GRCh38.p14 chr 2 NC_000002.12:g.130139608G>T
GRCh37.p13 chr 2 NC_000002.11:g.130897181G>A
GRCh37.p13 chr 2 NC_000002.11:g.130897181G>T
GRCh38.p14 chr 2 novel patch HSCHR2_12_CTG7_2 NW_025791762.1:g.316168G>A
GRCh38.p14 chr 2 novel patch HSCHR2_12_CTG7_2 NW_025791762.1:g.316168G>T
Gene: CCDC74B, coiled-coil domain containing 74B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CCDC74B transcript variant 1 NM_207310.4:c.1090C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform 1 NP_997193.1:p.Gln364Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant 1 NM_207310.4:c.1090C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform 1 NP_997193.1:p.Gln364Lys Q (Gln) > K (Lys) Missense Variant
CCDC74B transcript variant 2 NM_001258307.2:c.892C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform 2 NP_001245236.1:p.Gln298Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant 2 NM_001258307.2:c.892C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform 2 NP_001245236.1:p.Gln298Lys Q (Gln) > K (Lys) Missense Variant
CCDC74B transcript variant 3 NR_165309.1:n.1175C>T N/A Non Coding Transcript Variant
CCDC74B transcript variant 3 NR_165309.1:n.1175C>A N/A Non Coding Transcript Variant
CCDC74B transcript variant X13 XM_011512147.2:c. N/A Genic Downstream Transcript Variant
CCDC74B transcript variant X8 XM_047446276.1:c. N/A Genic Downstream Transcript Variant
CCDC74B transcript variant X9 XM_047446277.1:c. N/A Genic Downstream Transcript Variant
CCDC74B transcript variant X12 XM_047446280.1:c. N/A Genic Downstream Transcript Variant
CCDC74B transcript variant X1 XM_011512142.3:c.1396C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X1 XP_011510444.1:p.Gln466Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant X1 XM_011512142.3:c.1396C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X1 XP_011510444.1:p.Gln466Lys Q (Gln) > K (Lys) Missense Variant
CCDC74B transcript variant X2 XM_006712833.3:c.1228C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X2 XP_006712896.1:p.Gln410Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant X2 XM_006712833.3:c.1228C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X2 XP_006712896.1:p.Gln410Lys Q (Gln) > K (Lys) Missense Variant
CCDC74B transcript variant X3 XM_005263840.3:c.1216C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X3 XP_005263897.1:p.Gln406Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant X3 XM_005263840.3:c.1216C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X3 XP_005263897.1:p.Gln406Lys Q (Gln) > K (Lys) Missense Variant
CCDC74B transcript variant X4 XM_006712834.4:c.1102C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X4 XP_006712897.1:p.Gln368Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant X4 XM_006712834.4:c.1102C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X4 XP_006712897.1:p.Gln368Lys Q (Gln) > K (Lys) Missense Variant
CCDC74B transcript variant X5 XM_006712835.3:c.1030C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X5 XP_006712898.1:p.Gln344Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant X5 XM_006712835.3:c.1030C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X5 XP_006712898.1:p.Gln344Lys Q (Gln) > K (Lys) Missense Variant
CCDC74B transcript variant X6 XM_005263842.3:c.1018C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X6 XP_005263899.1:p.Gln340Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant X6 XM_005263842.3:c.1018C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X6 XP_005263899.1:p.Gln340Lys Q (Gln) > K (Lys) Missense Variant
CCDC74B transcript variant X7 XM_006712837.3:c.904C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X7 XP_006712900.1:p.Gln302Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant X7 XM_006712837.3:c.904C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X7 XP_006712900.1:p.Gln302Lys Q (Gln) > K (Lys) Missense Variant
CCDC74B transcript variant X10 XM_047446278.1:c.832C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X10 XP_047302234.1:p.Gln278Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant X10 XM_047446278.1:c.832C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X10 XP_047302234.1:p.Gln278Lys Q (Gln) > K (Lys) Missense Variant
CCDC74B transcript variant X11 XM_047446279.1:c.832C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X10 XP_047302235.1:p.Gln278Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant X11 XM_047446279.1:c.832C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X10 XP_047302235.1:p.Gln278Lys Q (Gln) > K (Lys) Missense Variant
CCDC74B transcript variant X14 XM_047446281.1:c.634C>T Q [CAG] > * [TAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X13 XP_047302237.1:p.Gln212Ter Q (Gln) > * (Ter) Stop Gained
CCDC74B transcript variant X14 XM_047446281.1:c.634C>A Q [CAG] > K [AAG] Coding Sequence Variant
coiled-coil domain-containing protein 74B isoform X13 XP_047302237.1:p.Gln212Lys Q (Gln) > K (Lys) Missense Variant
Gene: MED15P9, mediator complex subunit 15 pseudogene 9 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
MED15P9 transcript NR_033903.1:n. N/A Downstream 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.130139608= NC_000002.12:g.130139608G>A NC_000002.12:g.130139608G>T
GRCh37.p13 chr 2 NC_000002.11:g.130897181= NC_000002.11:g.130897181G>A NC_000002.11:g.130897181G>T
GRCh38.p14 chr 2 novel patch HSCHR2_12_CTG7_2 NW_025791762.1:g.316168= NW_025791762.1:g.316168G>A NW_025791762.1:g.316168G>T
CCDC74B transcript variant X4 XM_006712834.4:c.1102= XM_006712834.4:c.1102C>T XM_006712834.4:c.1102C>A
CCDC74B transcript variant X4 XM_006712834.3:c.1102= XM_006712834.3:c.1102C>T XM_006712834.3:c.1102C>A
CCDC74B transcript variant X4 XM_006712834.2:c.1102= XM_006712834.2:c.1102C>T XM_006712834.2:c.1102C>A
CCDC74B transcript variant X7 XM_006712834.1:c.1102= XM_006712834.1:c.1102C>T XM_006712834.1:c.1102C>A
CCDC74B transcript variant 1 NM_207310.4:c.1090= NM_207310.4:c.1090C>T NM_207310.4:c.1090C>A
CCDC74B transcript variant 1 NM_207310.3:c.1090= NM_207310.3:c.1090C>T NM_207310.3:c.1090C>A
CCDC74B transcript variant 1 NM_207310.2:c.1090= NM_207310.2:c.1090C>T NM_207310.2:c.1090C>A
CCDC74B transcript variant X1 XM_011512142.3:c.1396= XM_011512142.3:c.1396C>T XM_011512142.3:c.1396C>A
CCDC74B transcript variant X1 XM_011512142.2:c.1396= XM_011512142.2:c.1396C>T XM_011512142.2:c.1396C>A
CCDC74B transcript variant X1 XM_011512142.1:c.1396= XM_011512142.1:c.1396C>T XM_011512142.1:c.1396C>A
CCDC74B transcript variant X2 XM_006712833.3:c.1228= XM_006712833.3:c.1228C>T XM_006712833.3:c.1228C>A
CCDC74B transcript variant X2 XM_006712833.2:c.1228= XM_006712833.2:c.1228C>T XM_006712833.2:c.1228C>A
CCDC74B transcript variant X6 XM_006712833.1:c.1228= XM_006712833.1:c.1228C>T XM_006712833.1:c.1228C>A
CCDC74B transcript variant X3 XM_005263840.3:c.1216= XM_005263840.3:c.1216C>T XM_005263840.3:c.1216C>A
CCDC74B transcript variant X3 XM_005263840.2:c.1216= XM_005263840.2:c.1216C>T XM_005263840.2:c.1216C>A
CCDC74B transcript variant X3 XM_005263840.1:c.1216= XM_005263840.1:c.1216C>T XM_005263840.1:c.1216C>A
CCDC74B transcript variant X5 XM_006712835.3:c.1030= XM_006712835.3:c.1030C>T XM_006712835.3:c.1030C>A
CCDC74B transcript variant X5 XM_006712835.2:c.1030= XM_006712835.2:c.1030C>T XM_006712835.2:c.1030C>A
CCDC74B transcript variant X8 XM_006712835.1:c.1030= XM_006712835.1:c.1030C>T XM_006712835.1:c.1030C>A
CCDC74B transcript variant X7 XM_006712837.3:c.904= XM_006712837.3:c.904C>T XM_006712837.3:c.904C>A
CCDC74B transcript variant X7 XM_006712837.2:c.904= XM_006712837.2:c.904C>T XM_006712837.2:c.904C>A
CCDC74B transcript variant X10 XM_006712837.1:c.904= XM_006712837.1:c.904C>T XM_006712837.1:c.904C>A
CCDC74B transcript variant X6 XM_005263842.3:c.1018= XM_005263842.3:c.1018C>T XM_005263842.3:c.1018C>A
CCDC74B transcript variant X6 XM_005263842.2:c.1018= XM_005263842.2:c.1018C>T XM_005263842.2:c.1018C>A
CCDC74B transcript variant X5 XM_005263842.1:c.1018= XM_005263842.1:c.1018C>T XM_005263842.1:c.1018C>A
CCDC74B transcript variant 2 NM_001258307.2:c.892= NM_001258307.2:c.892C>T NM_001258307.2:c.892C>A
CCDC74B transcript variant 2 NM_001258307.1:c.892= NM_001258307.1:c.892C>T NM_001258307.1:c.892C>A
CCDC74B transcript variant X11 XM_047446279.1:c.832= XM_047446279.1:c.832C>T XM_047446279.1:c.832C>A
CCDC74B transcript variant X10 XM_047446278.1:c.832= XM_047446278.1:c.832C>T XM_047446278.1:c.832C>A
CCDC74B transcript variant 3 NR_165309.1:n.1175= NR_165309.1:n.1175C>T NR_165309.1:n.1175C>A
CCDC74B transcript variant X14 XM_047446281.1:c.634= XM_047446281.1:c.634C>T XM_047446281.1:c.634C>A
coiled-coil domain-containing protein 74B isoform X4 XP_006712897.1:p.Gln368= XP_006712897.1:p.Gln368Ter XP_006712897.1:p.Gln368Lys
coiled-coil domain-containing protein 74B isoform 1 NP_997193.1:p.Gln364= NP_997193.1:p.Gln364Ter NP_997193.1:p.Gln364Lys
coiled-coil domain-containing protein 74B isoform X1 XP_011510444.1:p.Gln466= XP_011510444.1:p.Gln466Ter XP_011510444.1:p.Gln466Lys
coiled-coil domain-containing protein 74B isoform X2 XP_006712896.1:p.Gln410= XP_006712896.1:p.Gln410Ter XP_006712896.1:p.Gln410Lys
coiled-coil domain-containing protein 74B isoform X3 XP_005263897.1:p.Gln406= XP_005263897.1:p.Gln406Ter XP_005263897.1:p.Gln406Lys
coiled-coil domain-containing protein 74B isoform X5 XP_006712898.1:p.Gln344= XP_006712898.1:p.Gln344Ter XP_006712898.1:p.Gln344Lys
coiled-coil domain-containing protein 74B isoform X7 XP_006712900.1:p.Gln302= XP_006712900.1:p.Gln302Ter XP_006712900.1:p.Gln302Lys
coiled-coil domain-containing protein 74B isoform X6 XP_005263899.1:p.Gln340= XP_005263899.1:p.Gln340Ter XP_005263899.1:p.Gln340Lys
coiled-coil domain-containing protein 74B isoform 2 NP_001245236.1:p.Gln298= NP_001245236.1:p.Gln298Ter NP_001245236.1:p.Gln298Lys
coiled-coil domain-containing protein 74B isoform X10 XP_047302235.1:p.Gln278= XP_047302235.1:p.Gln278Ter XP_047302235.1:p.Gln278Lys
coiled-coil domain-containing protein 74B isoform X10 XP_047302234.1:p.Gln278= XP_047302234.1:p.Gln278Ter XP_047302234.1:p.Gln278Lys
coiled-coil domain-containing protein 74B isoform X13 XP_047302237.1:p.Gln212= XP_047302237.1:p.Gln212Ter XP_047302237.1:p.Gln212Lys
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#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2732972211 Nov 08, 2017 (151)
2 gnomAD - Exomes NC_000002.11 - 130897181 Jul 13, 2019 (153)
3 ALFA NC_000002.12 - 130139608 Apr 26, 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
ss2732972211 NC_000002.11:130897180:G:A NC_000002.12:130139607:G:A (self)
2029112, ss2732972211 NC_000002.11:130897180:G:T NC_000002.12:130139607:G:T (self)
15151374946 NC_000002.12:130139607:G:T NC_000002.12:130139607: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 rs1490115279

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