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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.

rs780248745

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:101037191 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.00032 (9/28258, 14KJPN)
C=0.00012 (2/16012, ALFA)
C=0.0585 (171/2922, KOREAN) (+ 3 more)
C=0.0033 (6/1830, Korea1K)
G=0.50 (15/30, SGDP_PRJ)
C=0.50 (15/30, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MUC17 : Missense 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 16012 G=0.99988 A=0.00000, C=0.00012, T=0.00000
European Sub 11982 G=0.99983 A=0.00000, C=0.00017, T=0.00000
African Sub 2646 G=1.0000 A=0.0000, C=0.0000, T=0.0000
African Others Sub 94 G=1.00 A=0.00, C=0.00, T=0.00
African American Sub 2552 G=1.0000 A=0.0000, C=0.0000, T=0.0000
Asian Sub 98 G=1.00 A=0.00, C=0.00, T=0.00
East Asian Sub 80 G=1.00 A=0.00, C=0.00, T=0.00
Other Asian Sub 18 G=1.00 A=0.00, C=0.00, T=0.00
Latin American 1 Sub 140 G=1.000 A=0.000, C=0.000, T=0.000
Latin American 2 Sub 604 G=1.000 A=0.000, C=0.000, T=0.000
South Asian Sub 88 G=1.00 A=0.00, C=0.00, T=0.00
Other Sub 454 G=1.000 A=0.000, C=0.000, T=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
14KJPN JAPANESE Study-wide 28258 G=0.99968 C=0.00032
Allele Frequency Aggregator Total Global 16012 G=0.99988 A=0.00000, C=0.00012, T=0.00000
Allele Frequency Aggregator European Sub 11982 G=0.99983 A=0.00000, C=0.00017, T=0.00000
Allele Frequency Aggregator African Sub 2646 G=1.0000 A=0.0000, C=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 604 G=1.000 A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator Other Sub 454 G=1.000 A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 140 G=1.000 A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 98 G=1.00 A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 88 G=1.00 A=0.00, C=0.00, T=0.00
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9415 C=0.0585
Korean Genome Project KOREAN Study-wide 1830 G=0.9967 C=0.0033
SGDP_PRJ Global Study-wide 30 G=0.50 C=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.101037191G>A
GRCh38.p14 chr 7 NC_000007.14:g.101037191G>C
GRCh38.p14 chr 7 NC_000007.14:g.101037191G>T
GRCh37.p13 chr 7 NC_000007.13:g.100680472G>A
GRCh37.p13 chr 7 NC_000007.13:g.100680472G>C
GRCh37.p13 chr 7 NC_000007.13:g.100680472G>T
MUC17 RefSeqGene NG_050729.1:g.22116G>A
MUC17 RefSeqGene NG_050729.1:g.22116G>C
MUC17 RefSeqGene NG_050729.1:g.22116G>T
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.5775G>A R [AGG] > R [AGA] Coding Sequence Variant
mucin-17 precursor NP_001035194.1:p.Arg1925= R (Arg) > R (Arg) Synonymous Variant
MUC17 transcript variant 1 NM_001040105.2:c.5775G>C R [AGG] > S [AGC] Coding Sequence Variant
mucin-17 precursor NP_001035194.1:p.Arg1925S…

NP_001035194.1:p.Arg1925Ser

R (Arg) > S (Ser) Missense Variant
MUC17 transcript variant 1 NM_001040105.2:c.5775G>T R [AGG] > S [AGT] Coding Sequence Variant
mucin-17 precursor NP_001035194.1:p.Arg1925S…

NP_001035194.1:p.Arg1925Ser

R (Arg) > S (Ser) Missense Variant
MUC17 transcript variant 2 NR_133665.2:n.5830G>A N/A Non Coding Transcript Variant
MUC17 transcript variant 2 NR_133665.2:n.5830G>C N/A Non Coding Transcript Variant
MUC17 transcript variant 2 NR_133665.2:n.5830G>T 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 T
GRCh38.p14 chr 7 NC_000007.14:g.101037191= NC_000007.14:g.101037191G>A NC_000007.14:g.101037191G>C NC_000007.14:g.101037191G>T
GRCh37.p13 chr 7 NC_000007.13:g.100680472= NC_000007.13:g.100680472G>A NC_000007.13:g.100680472G>C NC_000007.13:g.100680472G>T
MUC17 RefSeqGene NG_050729.1:g.22116= NG_050729.1:g.22116G>A NG_050729.1:g.22116G>C NG_050729.1:g.22116G>T
MUC17 transcript variant 1 NM_001040105.2:c.5775= NM_001040105.2:c.5775G>A NM_001040105.2:c.5775G>C NM_001040105.2:c.5775G>T
MUC17 transcript variant 1 NM_001040105.1:c.5775= NM_001040105.1:c.5775G>A NM_001040105.1:c.5775G>C NM_001040105.1:c.5775G>T
MUC17 transcript variant 2 NR_133665.2:n.5830= NR_133665.2:n.5830G>A NR_133665.2:n.5830G>C NR_133665.2:n.5830G>T
MUC17 transcript variant 2 NR_133665.1:n.5828= NR_133665.1:n.5828G>A NR_133665.1:n.5828G>C NR_133665.1:n.5828G>T
MUC17 transcript NM_001004430.1:c.5775= NM_001004430.1:c.5775G>A NM_001004430.1:c.5775G>C NM_001004430.1:c.5775G>T
mucin-17 precursor NP_001035194.1:p.Arg1925= NP_001035194.1:p.Arg1925= NP_001035194.1:p.Arg1925Ser NP_001035194.1:p.Arg1925Ser
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#.

10 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1688872508 Apr 01, 2015 (144)
2 EVA_EXAC ss1688872509 Apr 01, 2015 (144)
3 EVA_EXAC ss1688872510 Apr 01, 2015 (144)
4 GNOMAD ss2736647838 Nov 08, 2017 (151)
5 GNOMAD ss2747888237 Nov 08, 2017 (151)
6 SGDP_PRJ ss3868000790 Apr 26, 2020 (154)
7 KRGDB ss3915298825 Apr 26, 2020 (154)
8 KOGIC ss3962214385 Apr 26, 2020 (154)
9 EVA ss5375558731 Oct 13, 2022 (156)
10 TOMMO_GENOMICS ss5725444795 Oct 13, 2022 (156)
11 ExAC

Submission ignored due to conflicting rows:
Row 8948781 (NC_000007.13:100680471:G:G 120892/120894, NC_000007.13:100680471:G:A 2/120894)
Row 8948782 (NC_000007.13:100680471:G:G 120893/120894, NC_000007.13:100680471:G:C 1/120894)
Row 8948783 (NC_000007.13:100680471:G:G 120893/120894, NC_000007.13:100680471:G:T 1/120894)

- Oct 12, 2018 (152)
12 ExAC

Submission ignored due to conflicting rows:
Row 8948781 (NC_000007.13:100680471:G:G 120892/120894, NC_000007.13:100680471:G:A 2/120894)
Row 8948782 (NC_000007.13:100680471:G:G 120893/120894, NC_000007.13:100680471:G:C 1/120894)
Row 8948783 (NC_000007.13:100680471:G:G 120893/120894, NC_000007.13:100680471:G:T 1/120894)

- Oct 12, 2018 (152)
13 ExAC

Submission ignored due to conflicting rows:
Row 8948781 (NC_000007.13:100680471:G:G 120892/120894, NC_000007.13:100680471:G:A 2/120894)
Row 8948782 (NC_000007.13:100680471:G:G 120893/120894, NC_000007.13:100680471:G:C 1/120894)
Row 8948783 (NC_000007.13:100680471:G:G 120893/120894, NC_000007.13:100680471:G:T 1/120894)

- Oct 12, 2018 (152)
14 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 5811126 (NC_000007.13:100680471:G:G 249382/249384, NC_000007.13:100680471:G:A 2/249384)
Row 5811127 (NC_000007.13:100680471:G:G 249383/249384, NC_000007.13:100680471:G:C 1/249384)
Row 5811128 (NC_000007.13:100680471:G:G 249383/249384, NC_000007.13:100680471:G:T 1/249384)

- Jul 13, 2019 (153)
15 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 5811126 (NC_000007.13:100680471:G:G 249382/249384, NC_000007.13:100680471:G:A 2/249384)
Row 5811127 (NC_000007.13:100680471:G:G 249383/249384, NC_000007.13:100680471:G:C 1/249384)
Row 5811128 (NC_000007.13:100680471:G:G 249383/249384, NC_000007.13:100680471:G:T 1/249384)

- Jul 13, 2019 (153)
16 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 5811126 (NC_000007.13:100680471:G:G 249382/249384, NC_000007.13:100680471:G:A 2/249384)
Row 5811127 (NC_000007.13:100680471:G:G 249383/249384, NC_000007.13:100680471:G:C 1/249384)
Row 5811128 (NC_000007.13:100680471:G:G 249383/249384, NC_000007.13:100680471:G:T 1/249384)

- Jul 13, 2019 (153)
17 KOREAN population from KRGDB NC_000007.13 - 100680472 Apr 26, 2020 (154)
18 Korean Genome Project NC_000007.14 - 101037191 Apr 26, 2020 (154)
19 SGDP_PRJ NC_000007.13 - 100680472 Apr 26, 2020 (154)
20 14KJPN NC_000007.14 - 101037191 Oct 13, 2022 (156)
21 ALFA NC_000007.14 - 101037191 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
ss1688872509, ss2736647838 NC_000007.13:100680471:G:A NC_000007.14:101037190:G:A (self)
6305163772 NC_000007.14:101037190:G:A NC_000007.14:101037190:G:A (self)
22476219, 20017770, ss1688872508, ss2736647838, ss2747888237, ss3868000790, ss3915298825, ss5375558731 NC_000007.13:100680471:G:C NC_000007.14:101037190:G:C (self)
18592386, 59281899, 6305163772, ss3962214385, ss5725444795 NC_000007.14:101037190:G:C NC_000007.14:101037190:G:C (self)
ss1688872510, ss2736647838 NC_000007.13:100680471:G:T NC_000007.14:101037190:G:T (self)
6305163772 NC_000007.14:101037190:G:T NC_000007.14:101037190: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 rs780248745

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