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dbSNP Short Genetic Variations

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.

rs756907429

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:74036106-74036107 (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
dupC
Variation Type
Indel Insertion and Deletion
Frequency
dupC=0.000045 (12/264690, TOPMED)
dupC=0.000004 (1/248768, GnomAD_exome)
dupC=0.000050 (7/140226, GnomAD) (+ 3 more)
dupC=0.000025 (3/121212, ExAC)
dupC=0.00000 (0/14050, ALFA)
dupC=0.00024 (3/12506, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PML : Intron 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 14050 CC=1.00000 CCC=0.00000
European Sub 9690 CC=1.0000 CCC=0.0000
African Sub 2898 CC=1.0000 CCC=0.0000
African Others Sub 114 CC=1.000 CCC=0.000
African American Sub 2784 CC=1.0000 CCC=0.0000
Asian Sub 112 CC=1.000 CCC=0.000
East Asian Sub 86 CC=1.00 CCC=0.00
Other Asian Sub 26 CC=1.00 CCC=0.00
Latin American 1 Sub 146 CC=1.000 CCC=0.000
Latin American 2 Sub 610 CC=1.000 CCC=0.000
South Asian Sub 98 CC=1.00 CCC=0.00
Other Sub 496 CC=1.000 CCC=0.000


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 -

No frequency provided

dupC=0.000045
gnomAD - Exomes Global Study-wide 248768 -

No frequency provided

dupC=0.000004
gnomAD - Exomes European Sub 132818 -

No frequency provided

dupC=0.000000
gnomAD - Exomes Asian Sub 48998 -

No frequency provided

dupC=0.00000
gnomAD - Exomes American Sub 34564 -

No frequency provided

dupC=0.00000
gnomAD - Exomes African Sub 16218 -

No frequency provided

dupC=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10044 -

No frequency provided

dupC=0.00000
gnomAD - Exomes Other Sub 6126 -

No frequency provided

dupC=0.0000
gnomAD - Genomes Global Study-wide 140226 -

No frequency provided

dupC=0.000050
gnomAD - Genomes European Sub 75942 -

No frequency provided

dupC=0.00000
gnomAD - Genomes African Sub 42032 -

No frequency provided

dupC=0.00017
gnomAD - Genomes American Sub 13644 -

No frequency provided

dupC=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 -

No frequency provided

dupC=0.0000
gnomAD - Genomes East Asian Sub 3130 -

No frequency provided

dupC=0.0000
gnomAD - Genomes Other Sub 2154 -

No frequency provided

dupC=0.0000
ExAC Global Study-wide 121212 -

No frequency provided

dupC=0.000025
ExAC Europe Sub 73240 -

No frequency provided

dupC=0.00000
ExAC Asian Sub 25136 -

No frequency provided

dupC=0.00000
ExAC American Sub 11568 -

No frequency provided

dupC=0.00000
ExAC African Sub 10360 -

No frequency provided

dupC=0.00029
ExAC Other Sub 908 -

No frequency provided

dupC=0.000
Allele Frequency Aggregator Total Global 14050 CC=1.00000 dupC=0.00000
Allele Frequency Aggregator European Sub 9690 CC=1.0000 dupC=0.0000
Allele Frequency Aggregator African Sub 2898 CC=1.0000 dupC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 CC=1.000 dupC=0.000
Allele Frequency Aggregator Other Sub 496 CC=1.000 dupC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 CC=1.000 dupC=0.000
Allele Frequency Aggregator Asian Sub 112 CC=1.000 dupC=0.000
Allele Frequency Aggregator South Asian Sub 98 CC=1.00 dupC=0.00
GO Exome Sequencing Project Global Study-wide 12506 -

No frequency provided

dupC=0.00024
GO Exome Sequencing Project European American Sub 8244 -

No frequency provided

dupC=0.0000
GO Exome Sequencing Project African American Sub 4262 -

No frequency provided

dupC=0.0007
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.74036107dup
GRCh37.p13 chr 15 NC_000015.9:g.74328448dup
PML RefSeqGene (LRG_1069) NG_029036.1:g.46435dup
Gene: PML, PML nuclear body scaffold (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PML transcript variant 6 NM_002675.4:c.1710+1577dup N/A Intron Variant
PML transcript variant 1 NM_033238.3:c.1710+1577dup N/A Intron Variant
PML transcript variant 7 NM_033246.3:c.*35+1577dup N/A Intron Variant
PML transcript variant 10 NM_033249.3:c.1566+1577dup N/A Intron Variant
PML transcript variant 5 NM_033244.4:c.*970_*971= N/A 3 Prime UTR Variant
PML transcript variant 2 NM_033240.3:c.*1450_*1451= N/A 3 Prime UTR Variant
PML transcript variant 8 NM_033247.3:c.*46_*47= N/A 3 Prime UTR Variant
PML transcript variant 11 NM_033250.3:c.*155_*156= N/A 3 Prime UTR Variant
PML transcript variant 9 NM_033239.3:c.*155_*156= N/A 3 Prime UTR 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 CC= dupC
GRCh38.p14 chr 15 NC_000015.10:g.74036106_74036107= NC_000015.10:g.74036107dup
GRCh37.p13 chr 15 NC_000015.9:g.74328447_74328448= NC_000015.9:g.74328448dup
PML RefSeqGene (LRG_1069) NG_029036.1:g.46434_46435= NG_029036.1:g.46435dup
PML transcript variant 5 NM_033244.4:c.*970_*971= NM_033244.4:c.*971dup
PML transcript variant 5 NM_033244.3:c.*970_*971= NM_033244.3:c.*971dup
PML transcript variant 2 NM_033240.3:c.*1450_*1451= NM_033240.3:c.*1451dup
PML transcript variant 2 NM_033240.2:c.*1450_*1451= NM_033240.2:c.*1451dup
PML transcript variant 9 NM_033239.3:c.*155_*156= NM_033239.3:c.*156dup
PML transcript variant 9 NM_033239.2:c.*155_*156= NM_033239.2:c.*156dup
PML transcript variant 11 NM_033250.3:c.*155_*156= NM_033250.3:c.*156dup
PML transcript variant 11 NM_033250.2:c.*155_*156= NM_033250.2:c.*156dup
PML transcript variant 8 NM_033247.3:c.*46_*47= NM_033247.3:c.*47dup
PML transcript variant 8 NM_033247.2:c.*46_*47= NM_033247.2:c.*47dup
PML transcript variant 12 NM_033245.2:c.*1435_*1436= NM_033245.2:c.*1436dup
PML transcript variant 3 NM_033242.2:c.*155_*156= NM_033242.2:c.*156dup
PML transcript variant 12 NM_033245.1:c.*1435_*1436= NM_033245.1:c.*1436dup
PML transcript variant 3 NM_033242.1:c.*155_*156= NM_033242.1:c.*156dup
PML transcript variant 6 NM_002675.3:c.1710+1576= NM_002675.3:c.1710+1577dup
PML transcript variant 6 NM_002675.4:c.1710+1576= NM_002675.4:c.1710+1577dup
PML transcript variant 1 NM_033238.2:c.1710+1576= NM_033238.2:c.1710+1577dup
PML transcript variant 1 NM_033238.3:c.1710+1576= NM_033238.3:c.1710+1577dup
PML transcript variant 7 NM_033246.2:c.*35+1576= NM_033246.2:c.*35+1577dup
PML transcript variant 7 NM_033246.3:c.*35+1576= NM_033246.3:c.*35+1577dup
PML transcript variant 10 NM_033249.2:c.1566+1576= NM_033249.2:c.1566+1577dup
PML transcript variant 10 NM_033249.3:c.1566+1576= NM_033249.3:c.1566+1577dup
PML transcript variant X1 XM_005254451.1:c.1566+1576= XM_005254451.1:c.1566+1577dup
PML transcript variant X3 XM_005254453.1:c.1710+1576= XM_005254453.1:c.1710+1577dup
PML transcript variant X4 XM_005254454.1:c.1711-884= XM_005254454.1:c.1711-883dup
PML transcript variant X5 XM_005254455.1:c.1710+1576= XM_005254455.1:c.1710+1577dup
PML transcript variant X7 XM_005254457.1:c.*35+1576= XM_005254457.1:c.*35+1577dup
PML transcript variant X10 XM_005254460.1:c.*36-884= XM_005254460.1:c.*36-883dup
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, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1712086265 Apr 01, 2015 (144)
2 GNOMAD ss2741388388 Nov 08, 2017 (151)
3 GNOMAD ss2749347573 Nov 08, 2017 (151)
4 GNOMAD ss2936746596 Nov 08, 2017 (151)
5 EVA ss3824938303 Apr 27, 2020 (154)
6 TOPMED ss4997060223 Apr 27, 2021 (155)
7 ExAC NC_000015.9 - 74328447 Oct 12, 2018 (152)
8 gnomAD - Genomes NC_000015.10 - 74036106 Apr 27, 2021 (155)
9 gnomAD - Exomes NC_000015.9 - 74328447 Jul 13, 2019 (153)
10 GO Exome Sequencing Project NC_000015.9 - 74328447 Oct 12, 2018 (152)
11 TopMed NC_000015.10 - 74036106 Apr 27, 2021 (155)
12 ALFA NC_000015.10 - 74036106 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
2300035, 10656351, 1395559, ss1712086265, ss2741388388, ss2749347573, ss2936746596, ss3824938303 NC_000015.9:74328446::C NC_000015.10:74036105:CC:CCC (self)
473790595, 212605883, ss4997060223 NC_000015.10:74036105::C NC_000015.10:74036105:CC:CCC (self)
3435226413 NC_000015.10:74036105:CC:CCC NC_000015.10:74036105:CC:CCC (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 rs756907429

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