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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.

rs35450564

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:50673185 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000990 (262/264690, TOPMED)
T=0.000189 (46/243450, GnomAD_exome)
T=0.000821 (115/140124, GnomAD) (+ 10 more)
T=0.000221 (26/117890, ExAC)
T=0.00007 (2/28258, 14KJPN)
T=0.00026 (6/23038, ALFA)
T=0.00006 (1/16760, 8.3KJPN)
T=0.00077 (10/13006, GO-ESP)
T=0.0005 (3/6404, 1000G_30x)
T=0.0004 (2/5008, 1000G)
T=0.010 (1/102, PharmGKB)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ABCC3 : 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 23038 C=0.99974 T=0.00026
European Sub 15752 C=1.00000 T=0.00000
African Sub 3492 C=0.9989 T=0.0011
African Others Sub 122 C=1.000 T=0.000
African American Sub 3370 C=0.9988 T=0.0012
Asian Sub 168 C=1.000 T=0.000
East Asian Sub 112 C=1.000 T=0.000
Other Asian Sub 56 C=1.00 T=0.00
Latin American 1 Sub 146 C=0.986 T=0.014
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 2772 C=1.0000 T=0.0000


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 C=0.999010 T=0.000990
gnomAD - Exomes Global Study-wide 243450 C=0.999811 T=0.000189
gnomAD - Exomes European Sub 128900 C=0.999984 T=0.000016
gnomAD - Exomes Asian Sub 48630 C=0.99996 T=0.00004
gnomAD - Exomes American Sub 34286 C=0.99988 T=0.00012
gnomAD - Exomes African Sub 15754 C=0.99759 T=0.00241
gnomAD - Exomes Ashkenazi Jewish Sub 9898 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 5982 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140124 C=0.999179 T=0.000821
gnomAD - Genomes European Sub 75896 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 41992 C=0.99774 T=0.00226
gnomAD - Genomes American Sub 13638 C=0.99868 T=0.00132
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3128 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2146 C=0.9991 T=0.0009
ExAC Global Study-wide 117890 C=0.999779 T=0.000221
ExAC Europe Sub 71038 C=0.99997 T=0.00003
ExAC Asian Sub 24694 C=0.99996 T=0.00004
ExAC American Sub 11358 C=0.99991 T=0.00009
ExAC African Sub 9920 C=0.9979 T=0.0021
ExAC Other Sub 880 C=0.999 T=0.001
14KJPN JAPANESE Study-wide 28258 C=0.99993 T=0.00007
Allele Frequency Aggregator Total Global 23038 C=0.99974 T=0.00026
Allele Frequency Aggregator European Sub 15752 C=1.00000 T=0.00000
Allele Frequency Aggregator African Sub 3492 C=0.9989 T=0.0011
Allele Frequency Aggregator Other Sub 2772 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 168 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.986 T=0.014
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
8.3KJPN JAPANESE Study-wide 16760 C=0.99994 T=0.00006
GO Exome Sequencing Project Global Study-wide 13006 C=0.99923 T=0.00077
GO Exome Sequencing Project European American Sub 8600 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9977 T=0.0023
1000Genomes_30x Global Study-wide 6404 C=0.9995 T=0.0005
1000Genomes_30x African Sub 1786 C=0.9994 T=0.0006
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=0.998 T=0.002
1000Genomes Global Study-wide 5008 C=0.9996 T=0.0004
1000Genomes African Sub 1322 C=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.999 T=0.001
PharmGKB Aggregated Global Study-wide 102 C=0.990 T=0.010
PharmGKB Aggregated PA129431304 Sub 102 C=0.990 T=0.010
SGDP_PRJ Global Study-wide 2 C=0.5 T=0.5
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 17 NC_000017.11:g.50673185C>T
GRCh37.p13 chr 17 NC_000017.10:g.48750546C>T
Gene: ABCC3, ATP binding cassette subfamily C member 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ABCC3 transcript variant 1 NM_003786.4:c.2409+47C>T N/A Intron Variant
ABCC3 transcript variant 2 NM_001144070.2:c. N/A Genic 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 C= T
GRCh38.p14 chr 17 NC_000017.11:g.50673185= NC_000017.11:g.50673185C>T
GRCh37.p13 chr 17 NC_000017.10:g.48750546= NC_000017.10:g.48750546C>T
ABCC3 transcript variant 1 NM_003786.3:c.2409+47= NM_003786.3:c.2409+47C>T
ABCC3 transcript variant 1 NM_003786.4:c.2409+47= NM_003786.4:c.2409+47C>T
ABCC3 transcript variant X1 XM_005257763.1:c.2217+47= XM_005257763.1:c.2217+47C>T
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#.

21 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 PHARMGKB_PMT ss69369118 May 16, 2007 (127)
2 1000GENOMES ss489117176 May 04, 2012 (137)
3 NHLBI-ESP ss713397025 Apr 25, 2013 (138)
4 PMT ss1026802446 Aug 21, 2014 (142)
5 JMKIDD_LAB ss1081092326 Aug 21, 2014 (142)
6 1000GENOMES ss1358863101 Aug 21, 2014 (142)
7 EVA_EXAC ss1692863014 Apr 01, 2015 (144)
8 HUMAN_LONGEVITY ss2217249184 Dec 20, 2016 (150)
9 GNOMAD ss2742851027 Nov 08, 2017 (151)
10 GNOMAD ss2749814767 Nov 08, 2017 (151)
11 GNOMAD ss2950506328 Nov 08, 2017 (151)
12 EVA ss3825131136 Apr 27, 2020 (154)
13 SGDP_PRJ ss3885862609 Apr 27, 2020 (154)
14 TOPMED ss5037840890 Apr 26, 2021 (155)
15 TOMMO_GENOMICS ss5222686332 Apr 26, 2021 (155)
16 1000G_HIGH_COVERAGE ss5303324870 Oct 16, 2022 (156)
17 EVA ss5427931204 Oct 16, 2022 (156)
18 HUGCELL_USP ss5496352236 Oct 16, 2022 (156)
19 1000G_HIGH_COVERAGE ss5607134341 Oct 16, 2022 (156)
20 TOMMO_GENOMICS ss5778984052 Oct 16, 2022 (156)
21 EVA ss5914142224 Oct 16, 2022 (156)
22 1000Genomes NC_000017.10 - 48750546 Oct 12, 2018 (152)
23 1000Genomes_30x NC_000017.11 - 50673185 Oct 16, 2022 (156)
24 ExAC NC_000017.10 - 48750546 Oct 12, 2018 (152)
25 gnomAD - Genomes NC_000017.11 - 50673185 Apr 26, 2021 (155)
26 gnomAD - Exomes NC_000017.10 - 48750546 Jul 13, 2019 (153)
27 GO Exome Sequencing Project NC_000017.10 - 48750546 Oct 12, 2018 (152)
28 PharmGKB Aggregated NC_000017.11 - 50673185 Apr 27, 2020 (154)
29 SGDP_PRJ NC_000017.10 - 48750546 Apr 27, 2020 (154)
30 8.3KJPN NC_000017.10 - 48750546 Apr 26, 2021 (155)
31 14KJPN NC_000017.11 - 50673185 Oct 16, 2022 (156)
32 TopMed NC_000017.11 - 50673185 Apr 26, 2021 (155)
33 ALFA NC_000017.11 - 50673185 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).

Associated ID History Updated (Build)
rs45442795 Mar 05, 2008 (129)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
72112912, 3312580, 12154802, 1588207, 37879589, 80655639, ss489117176, ss713397025, ss1026802446, ss1081092326, ss1358863101, ss1692863014, ss2742851027, ss2749814767, ss2950506328, ss3825131136, ss3885862609, ss5222686332, ss5427931204 NC_000017.10:48750545:C:T NC_000017.11:50673184:C:T (self)
94660276, 508856428, 5057, 112821156, 253386552, 8390829663, ss2217249184, ss5037840890, ss5303324870, ss5496352236, ss5607134341, ss5778984052, ss5914142224 NC_000017.11:50673184:C:T NC_000017.11:50673184:C:T (self)
ss69369118 NT_010783.15:14024697:C:T NC_000017.11:50673184: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.

No publications for rs35450564

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