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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.

rs41466049

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:16162 (GRCh38.p13) 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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.0134 (112/8379, 8.3KJPN)
G=0.0287 (84/2922, KOREAN)
G=0.0136 (27/1982, HGDP_Stanford) (+ 2 more)
G=0.020 (16/784, PRJEB37584)
A=0.2 (2/10, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MT-CYB : 500B Downstream Variant
MT-ND6 : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome
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.

Gene: MT-CYB, mitochondrially encoded cytochrome b (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.16162A>G N/A N/A
MT NC_012920.1:m.16162A>G N/A N/A
MT NC_012920.1:m.16162A>T N/A N/A
MT NC_012920.1:m.16162A>T N/A N/A
Gene: MT-ND6, mitochondrially encoded NADH dehydrogenase 6 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.16162A>G N/A N/A
MT NC_012920.1:m.16162A>G N/A N/A
MT NC_012920.1:m.16162A>T N/A N/A
MT NC_012920.1:m.16162A>T N/A N/A
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

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").

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Study Population Group Sample Size Ref Allele Alt Allele
8.3KJPN JAPANESE Study-wide 8379 A=0.9866 G=0.0134
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9713 G=0.0287
HGDP-CEPH-db Supplement 1 Global Study-wide 1982 A=0.9864 G=0.0136
HGDP-CEPH-db Supplement 1 Est_Asia Sub 460 A=0.957 G=0.043
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 394 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Middle_Est Sub 332 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Europe Sub 312 A=0.984 G=0.016
HGDP-CEPH-db Supplement 1 Africa Sub 238 A=0.992 G=0.008
HGDP-CEPH-db Supplement 1 America Sub 214 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 32 A=1.00 G=0.00
CNV burdens in cranial meningiomas Global Study-wide 784 A=0.980 G=0.020
CNV burdens in cranial meningiomas CRM Sub 784 A=0.980 G=0.020
SGDP_PRJ Global Study-wide 10 A=0.2 G=0.7, T=0.1
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 A= G T
MT NC_012920.1:m.16162= NC_012920.1:m.16162A>G NC_012920.1:m.16162A>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#.

23 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss66863440 Dec 01, 2006 (127)
2 ILLUMINA ss66931970 Dec 01, 2006 (127)
3 ILLUMINA ss68074748 Dec 12, 2006 (127)
4 ILLUMINA ss70458800 May 26, 2008 (130)
5 ILLUMINA ss70979340 May 17, 2007 (127)
6 ILLUMINA ss75875235 Dec 07, 2007 (129)
7 ILLUMINA ss152536615 Jul 15, 2010 (132)
8 ILLUMINA ss159102672 Jul 15, 2010 (132)
9 ILLUMINA ss169133787 Jul 15, 2010 (132)
10 ILLUMINA ss479152855 May 04, 2012 (137)
11 ILLUMINA ss484376881 May 04, 2012 (142)
12 ILLUMINA ss536559246 Jul 19, 2016 (147)
13 SSMP ss662653045 Oct 12, 2018 (152)
14 ILLUMINA ss780630579 Oct 12, 2018 (152)
15 ILLUMINA ss782634735 Oct 12, 2018 (152)
16 ILLUMINA ss836124383 Oct 12, 2018 (152)
17 SWEGEN ss3020999703 Oct 12, 2018 (152)
18 HGDP ss3847966518 Apr 27, 2020 (154)
19 SGDP_PRJ ss3892820141 Apr 27, 2020 (154)
20 KRGDB ss3892822454 Apr 27, 2020 (154)
21 EVA ss3984774020 Apr 27, 2021 (155)
22 TOMMO_GENOMICS ss5236853206 Apr 27, 2021 (155)
23 EVA ss5237630471 Apr 27, 2021 (155)
24 HGDP-CEPH-db Supplement 1 NC_001807.4 - 16163 Apr 27, 2020 (154)
25 KOREAN population from KRGDB NC_001807.4 - 16163 Apr 27, 2020 (154)
26 CNV burdens in cranial meningiomas NC_012920.1 - 16162 Apr 27, 2021 (155)
27 SGDP_PRJ NC_012920.1 - 16162 Apr 27, 2020 (154)
28 8.3KJPN NC_012920.1 - 16162 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).

Associated ID History Updated (Build)
rs199557159 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
644410, 50801504, ss66863440, ss66931970, ss68074748, ss70458800, ss70979340, ss75875235, ss479152855, ss662653045, ss782634735, ss836124383, ss3847966518, ss3892822454 NC_001807.4:16162:A:G NC_012920.1:16161:A:G (self)
312721, 44837121, 94822513, ss152536615, ss159102672, ss169133787, ss484376881, ss536559246, ss780630579, ss3020999703, ss3892820141, ss3984774020, ss5236853206, ss5237630471 NC_012920.1:16161:A:G NC_012920.1:16161:A:G (self)
44837121, ss3892820141 NC_012920.1:16161:A:T NC_012920.1:16161:A: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 rs41466049

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

No flank sequence available

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.post596+ae089ad