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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.

rs139517964

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:101036780 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.003025 (755/249590, GnomAD_exome)
A=0.008860 (1217/137358, GnomAD)
A=0.003504 (425/121302, ExAC) (+ 11 more)
A=0.00125 (53/42434, ALFA)
A=0.00042 (12/28258, 14KJPN)
A=0.00060 (10/16758, 8.3KJPN)
A=0.00807 (105/13006, GO-ESP)
A=0.0092 (59/6404, 1000G_30x)
A=0.0088 (44/5008, 1000G)
A=0.0005 (1/1830, Korea1K)
A=0.002 (1/534, MGP)
A=0.028 (6/216, Qatari)
G=0.50 (6/12, SGDP_PRJ)
A=0.50 (6/12, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MUC17 : Synonymous 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 58788 G=0.99663 A=0.00337, C=0.00000
European Sub 40790 G=0.99968 A=0.00032, C=0.00000
African Sub 8178 G=0.9801 A=0.0199, C=0.0000
African Others Sub 296 G=0.990 A=0.010, C=0.000
African American Sub 7882 G=0.9797 A=0.0203, C=0.0000
Asian Sub 164 G=1.000 A=0.000, C=0.000
East Asian Sub 110 G=1.000 A=0.000, C=0.000
Other Asian Sub 54 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 496 G=0.990 A=0.010, C=0.000
Latin American 2 Sub 624 G=1.000 A=0.000, C=0.000
South Asian Sub 92 G=1.00 A=0.00, C=0.00
Other Sub 8444 G=0.9980 A=0.0020, C=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
gnomAD - Exomes Global Study-wide 249590 G=0.996975 A=0.003025
gnomAD - Exomes European Sub 134898 G=0.999481 A=0.000519
gnomAD - Exomes Asian Sub 48362 G=0.99680 A=0.00320
gnomAD - Exomes American Sub 34066 G=0.99795 A=0.00205
gnomAD - Exomes African Sub 16156 G=0.97289 A=0.02711
gnomAD - Exomes Ashkenazi Jewish Sub 10040 G=0.99960 A=0.00040
gnomAD - Exomes Other Sub 6068 G=0.9970 A=0.0030
gnomAD - Genomes Global Study-wide 137358 G=0.991140 A=0.008860
gnomAD - Genomes European Sub 74840 G=0.99971 A=0.00029
gnomAD - Genomes African Sub 40650 G=0.97242 A=0.02758
gnomAD - Genomes American Sub 13376 G=0.99611 A=0.00389
gnomAD - Genomes Ashkenazi Jewish Sub 3286 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3096 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2110 G=0.9896 A=0.0104
ExAC Global Study-wide 121302 G=0.996496 A=0.003504
ExAC Europe Sub 73294 G=0.99943 A=0.00057
ExAC Asian Sub 25122 G=0.99713 A=0.00287
ExAC American Sub 11574 G=0.99767 A=0.00233
ExAC African Sub 10404 G=0.97309 A=0.02691
ExAC Other Sub 908 G=0.996 A=0.004
Allele Frequency Aggregator Total Global 42434 G=0.99875 A=0.00125, C=0.00000
Allele Frequency Aggregator European Sub 30706 G=0.99964 A=0.00036, C=0.00000
Allele Frequency Aggregator Other Sub 7010 G=0.9984 A=0.0016, C=0.0000
Allele Frequency Aggregator African Sub 3342 G=0.9922 A=0.0078, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 624 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 496 G=0.990 A=0.010, C=0.000
Allele Frequency Aggregator Asian Sub 164 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 92 G=1.00 A=0.00, C=0.00
14KJPN JAPANESE Study-wide 28258 G=0.99958 A=0.00042
8.3KJPN JAPANESE Study-wide 16758 G=0.99940 A=0.00060
GO Exome Sequencing Project Global Study-wide 13006 G=0.99193 A=0.00807
GO Exome Sequencing Project European American Sub 8600 G=0.9992 A=0.0008
GO Exome Sequencing Project African American Sub 4406 G=0.9778 A=0.0222
1000Genomes_30x Global Study-wide 6404 G=0.9908 A=0.0092
1000Genomes_30x African Sub 1786 G=0.9698 A=0.0302
1000Genomes_30x Europe Sub 1266 G=0.9992 A=0.0008
1000Genomes_30x South Asian Sub 1202 G=0.9975 A=0.0025
1000Genomes_30x East Asian Sub 1170 G=0.9991 A=0.0009
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9912 A=0.0088
1000Genomes African Sub 1322 G=0.9697 A=0.0303
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=0.9990 A=0.0010
1000Genomes South Asian Sub 978 G=0.998 A=0.002
1000Genomes American Sub 694 G=1.000 A=0.000
Korean Genome Project KOREAN Study-wide 1830 G=0.9995 A=0.0005
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.998 A=0.002
Qatari Global Study-wide 216 G=0.972 A=0.028
SGDP_PRJ Global Study-wide 12 G=0.50 A=0.50
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 7 NC_000007.14:g.101036780G>A
GRCh38.p14 chr 7 NC_000007.14:g.101036780G>C
GRCh37.p13 chr 7 NC_000007.13:g.100680061G>A
GRCh37.p13 chr 7 NC_000007.13:g.100680061G>C
MUC17 RefSeqGene NG_050729.1:g.21705G>A
MUC17 RefSeqGene NG_050729.1:g.21705G>C
Gene: MUC17, mucin 17, cell surface associated (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MUC17 transcript variant 1 NM_001040105.2:c.5364G>A S [TCG] > S [TCA] Coding Sequence Variant
mucin-17 precursor NP_001035194.1:p.Ser1788= S (Ser) > S (Ser) Synonymous Variant
MUC17 transcript variant 1 NM_001040105.2:c.5364G>C S [TCG] > S [TCC] Coding Sequence Variant
mucin-17 precursor NP_001035194.1:p.Ser1788= S (Ser) > S (Ser) Synonymous Variant
MUC17 transcript variant 2 NR_133665.2:n.5419G>A N/A Non Coding Transcript Variant
MUC17 transcript variant 2 NR_133665.2:n.5419G>C 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.

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 C
GRCh38.p14 chr 7 NC_000007.14:g.101036780= NC_000007.14:g.101036780G>A NC_000007.14:g.101036780G>C
GRCh37.p13 chr 7 NC_000007.13:g.100680061= NC_000007.13:g.100680061G>A NC_000007.13:g.100680061G>C
MUC17 RefSeqGene NG_050729.1:g.21705= NG_050729.1:g.21705G>A NG_050729.1:g.21705G>C
MUC17 transcript variant 1 NM_001040105.2:c.5364= NM_001040105.2:c.5364G>A NM_001040105.2:c.5364G>C
MUC17 transcript variant 1 NM_001040105.1:c.5364= NM_001040105.1:c.5364G>A NM_001040105.1:c.5364G>C
MUC17 transcript variant 2 NR_133665.2:n.5419= NR_133665.2:n.5419G>A NR_133665.2:n.5419G>C
MUC17 transcript variant 2 NR_133665.1:n.5417= NR_133665.1:n.5417G>A NR_133665.1:n.5417G>C
MUC17 transcript NM_001004430.1:c.5364= NM_001004430.1:c.5364G>A NM_001004430.1:c.5364G>C
mucin-17 precursor NP_001035194.1:p.Ser1788= NP_001035194.1:p.Ser1788= NP_001035194.1:p.Ser1788=
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#.

29 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342242452 May 09, 2011 (134)
2 1000GENOMES ss459852540 Sep 17, 2011 (135)
3 1000GENOMES ss1326375561 Aug 21, 2014 (142)
4 EVA_EXAC ss1688872374 Apr 01, 2015 (144)
5 EVA_MGP ss1711174923 Apr 01, 2015 (144)
6 WEILL_CORNELL_DGM ss1927860180 Feb 12, 2016 (147)
7 HUMAN_LONGEVITY ss2296264619 Dec 20, 2016 (150)
8 GRF ss2708546457 Nov 08, 2017 (151)
9 GNOMAD ss2736647691 Nov 08, 2017 (151)
10 GNOMAD ss2747888164 Nov 08, 2017 (151)
11 GNOMAD ss2856883849 Nov 08, 2017 (151)
12 EVA ss3766935421 Jul 13, 2019 (153)
13 KHV_HUMAN_GENOMES ss3810105616 Jul 13, 2019 (153)
14 EVA ss3824302544 Apr 26, 2020 (154)
15 SGDP_PRJ ss3868000756 Apr 26, 2020 (154)
16 KOGIC ss3962214368 Apr 26, 2020 (154)
17 FSA-LAB ss3984375815 Apr 26, 2021 (155)
18 EVA ss3986393406 Apr 26, 2021 (155)
19 TOPMED ss4756895186 Apr 26, 2021 (155)
20 TOPMED ss4756895187 Apr 26, 2021 (155)
21 TOMMO_GENOMICS ss5184711465 Apr 26, 2021 (155)
22 1000G_HIGH_COVERAGE ss5274065962 Oct 13, 2022 (156)
23 EVA ss5375558672 Oct 13, 2022 (156)
24 EVA ss5509066693 Oct 13, 2022 (156)
25 1000G_HIGH_COVERAGE ss5562865180 Oct 13, 2022 (156)
26 SANFORD_IMAGENETICS ss5643604689 Oct 13, 2022 (156)
27 TOMMO_GENOMICS ss5725444729 Oct 13, 2022 (156)
28 EVA ss5860123677 Oct 13, 2022 (156)
29 EVA ss5972788494 Oct 13, 2022 (156)
30 1000Genomes NC_000007.13 - 100680061 Oct 12, 2018 (152)
31 1000Genomes_30x NC_000007.14 - 101036780 Oct 13, 2022 (156)
32 ExAC NC_000007.13 - 100680061 Oct 12, 2018 (152)
33 gnomAD - Genomes NC_000007.14 - 101036780 Apr 26, 2021 (155)
34 gnomAD - Exomes NC_000007.13 - 100680061 Jul 13, 2019 (153)
35 GO Exome Sequencing Project NC_000007.13 - 100680061 Oct 12, 2018 (152)
36 Korean Genome Project NC_000007.14 - 101036780 Apr 26, 2020 (154)
37 Medical Genome Project healthy controls from Spanish population NC_000007.13 - 100680061 Apr 26, 2020 (154)
38 Qatari NC_000007.13 - 100680061 Apr 26, 2020 (154)
39 SGDP_PRJ NC_000007.13 - 100680061 Apr 26, 2020 (154)
40 8.3KJPN NC_000007.13 - 100680061 Apr 26, 2021 (155)
41 14KJPN NC_000007.14 - 101036780 Oct 13, 2022 (156)
42 TopMed

Submission ignored due to conflicting rows:
Row 594272745 (NC_000007.14:101036779:G:A 2522/264690)
Row 594272746 (NC_000007.14:101036779:G:C 1/264690)

- Apr 26, 2021 (155)
43 TopMed

Submission ignored due to conflicting rows:
Row 594272745 (NC_000007.14:101036779:G:A 2522/264690)
Row 594272746 (NC_000007.14:101036779:G:C 1/264690)

- Apr 26, 2021 (155)
44 ALFA NC_000007.14 - 101036780 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
38390794, 8948636, 5810958, 760486, 290683, 9902110, 20017736, 42680772, ss342242452, ss459852540, ss1326375561, ss1688872374, ss1711174923, ss1927860180, ss2708546457, ss2736647691, ss2747888164, ss2856883849, ss3766935421, ss3824302544, ss3868000756, ss3984375815, ss3986393406, ss5184711465, ss5375558672, ss5509066693, ss5643604689, ss5972788494 NC_000007.13:100680060:G:A NC_000007.14:101036779:G:A (self)
50391115, 270933181, 18592369, 59281833, 9190978024, ss2296264619, ss3810105616, ss3962214368, ss4756895186, ss5274065962, ss5562865180, ss5725444729, ss5860123677 NC_000007.14:101036779:G:A NC_000007.14:101036779:G:A (self)
9190978024, ss2296264619, ss4756895187 NC_000007.14:101036779:G:C NC_000007.14:101036779:G:C (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 rs139517964

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