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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.

rs41479950

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:16163 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.0002 (2/8377, 8.3KJPN)
G=0.0120 (24/1998, HGDP_Stanford)
G=0.006 (5/778, PRJEB37584) (+ 2 more)
G=0.021 (11/534, MGP)
A=0.0 (0/4, 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.16163A>G N/A N/A
MT NC_012920.1:m.16163A>G 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.16163A>G N/A N/A
MT NC_012920.1:m.16163A>G 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 8377 A=0.9998 G=0.0002
HGDP-CEPH-db Supplement 1 Global Study-wide 1998 A=0.9880 G=0.0120
HGDP-CEPH-db Supplement 1 Est_Asia Sub 450 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 404 A=0.985 G=0.015
HGDP-CEPH-db Supplement 1 Middle_Est Sub 344 A=0.977 G=0.023
HGDP-CEPH-db Supplement 1 Europe Sub 310 A=0.968 G=0.032
HGDP-CEPH-db Supplement 1 Africa Sub 240 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 America Sub 216 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 34 A=1.00 G=0.00
CNV burdens in cranial meningiomas Global Study-wide 778 A=0.994 G=0.006
CNV burdens in cranial meningiomas CRM Sub 778 A=0.994 G=0.006
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.979 G=0.021
SGDP_PRJ Global Study-wide 4 A=0.0 G=1.0
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
MT NC_012920.1:m.16163= NC_012920.1:m.16163A>G
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#.

26 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss66863441 Dec 01, 2006 (127)
2 ILLUMINA ss66931972 Dec 01, 2006 (127)
3 ILLUMINA ss68074749 Dec 12, 2006 (127)
4 ILLUMINA ss70458801 May 24, 2008 (130)
5 ILLUMINA ss70979341 May 18, 2007 (127)
6 ILLUMINA ss75896379 Dec 06, 2007 (129)
7 ILLUMINA ss152536620 Jul 15, 2010 (132)
8 ILLUMINA ss159102673 Jul 15, 2010 (132)
9 ILLUMINA ss159849695 Jul 15, 2010 (132)
10 ILLUMINA ss169133802 Jul 15, 2010 (132)
11 ILLUMINA ss479152856 May 04, 2012 (137)
12 ILLUMINA ss479465450 Oct 12, 2018 (152)
13 ILLUMINA ss484376883 May 04, 2012 (142)
14 ILLUMINA ss536559247 Jul 19, 2016 (147)
15 ILLUMINA ss780630580 Oct 12, 2018 (152)
16 ILLUMINA ss782634736 Oct 12, 2018 (152)
17 ILLUMINA ss832615468 Jul 19, 2016 (147)
18 ILLUMINA ss833206157 Jul 19, 2016 (147)
19 ILLUMINA ss836124384 Oct 12, 2018 (152)
20 EVA_MGP ss1711595159 Jul 19, 2016 (147)
21 GRF ss2710056366 Oct 12, 2018 (152)
22 SWEGEN ss3020999704 Oct 12, 2018 (152)
23 HGDP ss3847966519 Apr 27, 2020 (154)
24 SGDP_PRJ ss3892820142 Apr 27, 2020 (154)
25 EVA ss3984774021 Apr 27, 2021 (155)
26 TOMMO_GENOMICS ss5236853207 Apr 27, 2021 (155)
27 HGDP-CEPH-db Supplement 1 NC_001807.4 - 16164 Apr 27, 2020 (154)
28 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 16163 Apr 27, 2020 (154)
29 CNV burdens in cranial meningiomas NC_012920.1 - 16163 Apr 27, 2021 (155)
30 SGDP_PRJ NC_012920.1 - 16163 Apr 27, 2020 (154)
31 8.3KJPN NC_012920.1 - 16163 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)
rs201155613 Aug 21, 2014 (142)
rs372321397 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
644411, ss159849695, ss479152856, ss479465450, ss782634736, ss836124384, ss3847966519 NC_001807.4:16163:A:G NC_012920.1:16162:A:G (self)
710919, 312722, 44837122, 94822514, ss66863441, ss66931972, ss68074749, ss70458801, ss70979341, ss75896379, ss152536620, ss159102673, ss169133802, ss484376883, ss536559247, ss780630580, ss832615468, ss833206157, ss1711595159, ss2710056366, ss3020999704, ss3892820142, ss3984774021, ss5236853207 NC_012920.1:16162:A:G NC_012920.1:16162:A:G (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 rs41479950

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