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Report date: 2022-02-02
View All FL Sequence Variants
FL Sequence Variants satisfying ClinGen BA1-BS1

Most Frequent Variants in Mitomap ("Top 40")

There are twelve variants with ≥50% overall frequency that are widespread across all lineages. These are shown in bold.

TABLE 1
Variants present at ≥80% in lineages L, M, or N are in yellow. Variants present at ≥50% are in light blue.

rCRS Position Allele HGVS Notation Overall Variant Count Overall Variant Frequency Variant Frequency in lineage L Variant Frequency in lineage M Variant Frequency in lineage N Ancestral SNP ††
A 15326 G m.15326A>G 53859 98.7% 99.5% 99.1% 98.4% Yes
A 8860 G m.8860A>G 53777 98.5% 99.0% 98.9% 98.3% Yes
A 750 G m.750A>G 53668 98.3% 95.2% 99.7% 98.4% Yes
A 4769 G m.4769A>G 53292 97.6% 99.0% 99.5% 96.8% Yes
A 263 G m.263A>G 51945 95.1% 81.6% 98.3% 96.4% Yes
A 1438 G m.1438A>G 51863 95.0% 81.4% 96.4% 96.8% Yes
C 7028 T m.7028C>T 43967 80.5% 99.7% 99.7% 71.3% Yes
A 2706 G m.2706A>G 43035 78.8% 90.8% 97.1% 71.1% Yes
G 11719 A m.11719G>A 42161 77.2% 99.7% 99.6% 66.4% Yes
C 14766 T m.14766C>T 41880 76.7% 99.7% 96.2% 66.7% Yes
A 73 G m.73A>G 41443 75.9% 85.3% 98.7% 67.1% Yes
A10398Gm.10398A>G2373043.5%95.4%99.5%17.1%Yes
C12705Tm.12705C>T2224140.7%99.5%99.1%12.5%Yes
C16223Tm.16223C>T2112238.7%92.0%94.6%12.1%Yes
A8701Gm.8701A>G1774832.5%99.3%99.1%0.3%Yes
T9540Cm.9540T>C1773532.5%99.7%99.5%0.1%Yes
T10873Cm.10873T>C1772332.5%99.6%99.3%0.1%Yes
G15301Am.15301G>A1536628.1%58.3%99.4%0.6%No
T489Cm.489T>C1410325.8%0.1%98.4%7.1%No
G15043Am.15043G>A1289023.6%1.8%99.3%3.2%No
C10400Tm.10400C>T1163021.3%0.1%99.6%0.0%No
T14783Cm.14783T>C1162121.3%0.0%99.3%0.1%No

TABLE 2
Additional variants present at ≥50% in lineages L, M, or N (in light blue), or in ≥10,000 sequences overall (in light beige)

rCRS Position Allele HGVS Notation Overall Variant Count Overall Variant Frequency Variant Frequency in lineage L Variant Frequency in lineage M Variant Frequency in lineage N Ancestral SNP ††
T 16519 C m.16519T>C 34370 63.0% 64.5% 55.0% 65.2% Yes
T310Cm.310T>C2241141.1%34.5%41.9%41.9%No
C315CCm.315_316insC1690831.0%37.7%27.7%30.9%No
C309CCTm.309_310insCT1450826.6%16.6%30.3%27.0%No
T152Cm.152T>C1399525.6%62.8%20.6%21.1%Yes
T16189Cm.16189T>C1385025.4%53.0%14.7%24.2%Yes
CA522dm.522_523delCA1268223.2%49.5%24.3%18.5%No
T146Cm.146T>C1067419.6%37.7%17.8%17.1%Yes
T16311Cm.16311T>C1062319.5%53.5%17.5%14.4%Yes
T195Cm.195T>C1031318.9%55.9%14.7%14.1%Yes
G1018Am.1018G>A40707.5%65.0%0.5%0.1%Yes
G7521Am.7521G>A40507.4%62.9%0.5%0.4%Yes
G769Am.769G>A40247.4%65.1%0.0%0.1%Yes
C7256Tm.7256C>T38877.1%63.1%0.2%0.0%Yes
C13650Tm.13650C>T38777.1%62.9%0.1%0.1%Yes
C3594Tm.3594C>T38637.1%63.0%0.0%0.0%Yes
A4104Gm.4104A>G38467.0%62.8%0.0%0.0%Yes
A13105Gm.13105A>G38177.0%55.4%1.1%0.8%Yes

Top Level Haplogroups of Lineages L, M, and N
  • Lineage L ("African"): L0, L1, L2, L3, L4, L5, L6
  • Lineage M ("Asian"): C, D, E, G, M, Q, Z
  • Lineage N ("Eurasian"): A, B, F, H, HV, I, J, K, N, O, P, R, S, T, U, V, W, X, Y

†† Ancestral SNPs are spread throughout the human mtDNA tree. These ancestral variants, the "RSRS50", are: 73G, 146C, 152C, 195C, 247A, 263G, 750G, 769A, 825A, 1018A, 1438G, 2706G, 2758A, 2885C, 3594T, 4104G, 4312T, 4769G, 7028T, 7146G, 7256T, 7521A, 8468T, 8655T, 8701G, 8860G, 9540C, 10398G, 10664T, 10688A, 10810C, 10873C, 10915C, 11719A, 11914A, 12705T, 13105G, 13276G, 13506T, 13650T, 14766T, 15326G, 16129A, 16187T, 16189C, 16223T, 16230G, 16278T, 16311C, 16519C. The most widespread across all lineages are shown in bold.

††† Additionally, the RSRS ancestor sequence has two single base deletions, 523d & 524d, which are located at the end of a string of CA repeats. Indels in this region are variously notated and common. The beginning of this particular CA repeat string is at position 514; an alternate call of “514_515d” for this 523_524d deletion is often used. These two deleted bases are not indexed in Mitomap's "RSRS50" set and are among those variants specifically excluded by Phylotree in the construction of their master tree.

Topic revision: r18 - 02 Feb 2022, UnknownUser

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