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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.

rs2307434

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:89326743 (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
delG
Variation Type
Deletion
Frequency
delG=0.009437 (2498/264690, TOPMED)
delG=0.002372 (596/251264, GnomAD_exome)
delG=0.008910 (1249/140184, GnomAD) (+ 5 more)
delG=0.002887 (350/121224, ExAC)
delG=0.00027 (12/44190, ALFA)
delG=0.00999 (125/12518, GO-ESP)
delG=0.0164 (105/6404, 1000G_30x)
delG=0.0138 (69/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MIR6766 : Non Coding Transcript Variant
POLG : Intron Variant
Publications
1 citation
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 44186 G=0.99973 =0.00027 0.999457 0.0 0.000543 0
European Sub 32612 G=1.00000 =0.00000 1.0 0.0 0.0 N/A
African Sub 3352 G=0.9976 =0.0024 0.995227 0.0 0.004773 0
African Others Sub 112 G=1.000 =0.000 1.0 0.0 0.0 N/A
African American Sub 3240 G=0.9975 =0.0025 0.995062 0.0 0.004938 0
Asian Sub 168 G=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 112 G=1.000 =0.000 1.0 0.0 0.0 N/A
Other Asian Sub 56 G=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 486 G=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 622 G=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 G=1.00 =0.00 1.0 0.0 0.0 N/A
Other Sub 6848 G=0.9994 =0.0006 0.998832 0.0 0.001168 0


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=0.990563 delG=0.009437
gnomAD - Exomes Global Study-wide 251264 G=0.997628 delG=0.002372
gnomAD - Exomes European Sub 135224 G=0.999978 delG=0.000022
gnomAD - Exomes Asian Sub 49004 G=0.99998 delG=0.00002
gnomAD - Exomes American Sub 34580 G=0.99832 delG=0.00168
gnomAD - Exomes African Sub 16246 G=0.96732 delG=0.03268
gnomAD - Exomes Ashkenazi Jewish Sub 10076 G=1.00000 delG=0.00000
gnomAD - Exomes Other Sub 6134 G=0.9995 delG=0.0005
gnomAD - Genomes Global Study-wide 140184 G=0.991090 delG=0.008910
gnomAD - Genomes European Sub 75916 G=0.99997 delG=0.00003
gnomAD - Genomes African Sub 42000 G=0.97176 delG=0.02824
gnomAD - Genomes American Sub 13662 G=0.99634 delG=0.00366
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 delG=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 delG=0.0000
gnomAD - Genomes Other Sub 2152 G=0.9949 delG=0.0051
ExAC Global Study-wide 121224 G=0.997113 delG=0.002887
ExAC Europe Sub 73224 G=1.00000 delG=0.00000
ExAC Asian Sub 25152 G=1.00000 delG=0.00000
ExAC American Sub 11564 G=0.99827 delG=0.00173
ExAC African Sub 10378 G=0.96820 delG=0.03180
ExAC Other Sub 906 G=1.000 delG=0.000
Allele Frequency Aggregator Total Global 44190 G=0.99968 delG=0.00027
Allele Frequency Aggregator European Sub 32612 G=1.00000 delG=0.00000
Allele Frequency Aggregator Other Sub 6850 G=0.9993 delG=0.0006
Allele Frequency Aggregator African Sub 3352 G=0.9976 delG=0.0024
Allele Frequency Aggregator Latin American 2 Sub 622 G=1.000 delG=0.000
Allele Frequency Aggregator Latin American 1 Sub 488 G=0.998 delG=0.000
Allele Frequency Aggregator Asian Sub 168 G=1.000 delG=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 delG=0.00
GO Exome Sequencing Project Global Study-wide 12518 G=0.99001 delG=0.00999
GO Exome Sequencing Project European American Sub 8254 G=1.0000 delG=0.0000
GO Exome Sequencing Project African American Sub 4264 G=0.9707 delG=0.0293
1000Genomes_30x Global Study-wide 6404 G=0.9836 delG=0.0164
1000Genomes_30x African Sub 1786 G=0.9434 delG=0.0566
1000Genomes_30x Europe Sub 1266 G=1.0000 delG=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 delG=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 delG=0.0000
1000Genomes_30x American Sub 980 G=0.996 delG=0.004
1000Genomes Global Study-wide 5008 G=0.9862 delG=0.0138
1000Genomes African Sub 1322 G=0.9501 delG=0.0499
1000Genomes East Asian Sub 1008 G=1.0000 delG=0.0000
1000Genomes Europe Sub 1006 G=1.0000 delG=0.0000
1000Genomes South Asian Sub 978 G=1.000 delG=0.000
1000Genomes American Sub 694 G=0.996 delG=0.004
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 15 NC_000015.10:g.89326743del
GRCh37.p13 chr 15 NC_000015.9:g.89869974del
POLG RefSeqGene (LRG_765) NG_008218.2:g.13053del
Gene: POLG, DNA polymerase gamma, catalytic subunit (minus strand)
Molecule type Change Amino acid[Codon] SO Term
POLG transcript variant 2 NM_001126131.2:c.1586-5del N/A Intron Variant
POLG transcript variant 1 NM_002693.3:c.1586-5del N/A Intron Variant
Gene: MIR6766, microRNA 6766 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MIR6766 transcript NR_106824.1:n.68del 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.

Allele: delG (allele ID: 196240 )
ClinVar Accession Disease Names Clinical Significance
RCV000180588.7 not specified Benign
RCV000466342.10 Progressive sclerosing poliodystrophy Benign
RCV000717665.2 Seizure Benign
RCV001812160.3 not provided Benign
RCV001847820.2 Hereditary spastic paraplegia Likely-Benign
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= delG
GRCh38.p14 chr 15 NC_000015.10:g.89326743= NC_000015.10:g.89326743del
GRCh37.p13 chr 15 NC_000015.9:g.89869974= NC_000015.9:g.89869974del
POLG RefSeqGene (LRG_765) NG_008218.2:g.13053= NG_008218.2:g.13053del
MIR6766 transcript NR_106824.1:n.68= NR_106824.1:n.68del
POLG transcript variant 2 NM_001126131.1:c.1586-5= NM_001126131.1:c.1586-5del
POLG transcript variant 2 NM_001126131.2:c.1586-5= NM_001126131.2:c.1586-5del
POLG transcript variant 1 NM_002693.2:c.1586-5= NM_002693.2:c.1586-5del
POLG transcript variant 1 NM_002693.3:c.1586-5= NM_002693.3:c.1586-5del
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#.

23 SubSNP, 8 Frequency, 5 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss4388327 May 29, 2002 (106)
2 1000GENOMES ss328176034 May 09, 2011 (138)
3 1000GENOMES ss498992121 May 04, 2012 (138)
4 LUNTER ss552768920 Apr 25, 2013 (138)
5 1000GENOMES ss1375259659 Aug 21, 2014 (142)
6 EVA_EXAC ss1712090621 Apr 01, 2015 (144)
7 GNOMAD ss2741494996 Nov 08, 2017 (151)
8 GNOMAD ss2749380726 Nov 08, 2017 (151)
9 GNOMAD ss2938005832 Nov 08, 2017 (151)
10 AFFY ss2985050735 Nov 08, 2017 (151)
11 ILLUMINA ss3653822722 Oct 12, 2018 (152)
12 EVA_DECODE ss3698424089 Jul 13, 2019 (153)
13 KHV_HUMAN_GENOMES ss3818724475 Jul 13, 2019 (153)
14 EVA ss3824951969 Apr 27, 2020 (154)
15 EVA ss3834366253 Apr 27, 2020 (154)
16 EVA ss3986661671 Apr 27, 2021 (155)
17 TOPMED ss5000873744 Apr 27, 2021 (155)
18 1000G_HIGH_COVERAGE ss5299394345 Oct 17, 2022 (156)
19 HUGCELL_USP ss5493011624 Oct 17, 2022 (156)
20 1000G_HIGH_COVERAGE ss5601273812 Oct 17, 2022 (156)
21 SANFORD_IMAGENETICS ss5658043999 Oct 17, 2022 (156)
22 EVA ss5876963522 Oct 17, 2022 (156)
23 EVA ss5949466465 Oct 17, 2022 (156)
24 1000Genomes NC_000015.9 - 89869974 Oct 12, 2018 (152)
25 1000Genomes_30x NC_000015.10 - 89326743 Oct 17, 2022 (156)
26 ExAC NC_000015.9 - 89869974 Oct 12, 2018 (152)
27 gnomAD - Genomes NC_000015.10 - 89326743 Apr 27, 2021 (155)
28 gnomAD - Exomes NC_000015.9 - 89869974 Jul 13, 2019 (153)
29 GO Exome Sequencing Project NC_000015.9 - 89869974 Oct 12, 2018 (152)
30 TopMed NC_000015.10 - 89326743 Apr 27, 2021 (155)
31 ALFA NC_000015.10 - 89326743 Apr 27, 2021 (155)
32 ClinVar RCV000180588.7 Oct 17, 2022 (156)
33 ClinVar RCV000466342.10 Oct 17, 2022 (156)
34 ClinVar RCV000717665.2 Oct 17, 2022 (156)
35 ClinVar RCV001812160.3 Oct 17, 2022 (156)
36 ClinVar RCV001847820.2 Oct 17, 2022 (156)
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).

Associated ID History Updated (Build)
rs3176181 Jul 03, 2002 (106)
rs146034250 May 13, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss328176034, ss552768920 NC_000015.8:87670977:G: NC_000015.10:89326742:G: (self)
67653946, 2372140, 10763580, 1409206, ss498992121, ss1375259659, ss1712090621, ss2741494996, ss2749380726, ss2938005832, ss2985050735, ss3653822722, ss3824951969, ss3834366253, ss3986661671, ss5658043999, ss5949466465 NC_000015.9:89869973:G: NC_000015.10:89326742:G: (self)
RCV000180588.7, RCV000466342.10, RCV000717665.2, RCV001812160.3, RCV001847820.2, 88799747, 476983938, 216419404, 1042626065, ss3698424089, ss3818724475, ss5000873744, ss5299394345, ss5493011624, ss5601273812, ss5876963522 NC_000015.10:89326742:G: NC_000015.10:89326742:G: (self)
ss4388327 NT_010274.17:4835500:G: NC_000015.10:89326742:G: (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 rs2307434
PMID Title Author Year Journal
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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.post825+45319f0