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View All FL Sequence Variants FL Sequence Variants satisfying ClinGen BA1-BS1

Most Frequent Variants in Mitomap ("Top 42")

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	8860	G	m.8860A>G	64628	99.0%	99.3%	99.3%	98.9%	Yes
A	15326	G	m.15326A>G	64527	98.9%	99.6%	98.9%	98.7%	Yes
A	750	G	m.750A>G	64323	98.6%	95.4%	99.8%	98.7%	Yes
A	4769	G	m.4769A>G	63951	98.0%	99.2%	99.5%	97.3%	Yes
A	263	G	m.263A>G	62661	96.0%	84.4%	98.5%	97.1%	Yes
A	1438	G	m.1438A>G	62349	95.5%	82.9%	96.9%	97.2%	Yes
C	7028	T	m.7028C>T	52379	80.3%	99.8%	99.5%	71.1%	Yes
A	2706	G	m.2706A>G	51492	78.9%	92.5%	97.6%	70.9%	Yes
G	11719	A	m.11719G>A	50310	77.1%	99.8%	99.9%	66.3%	Yes
C	14766	T	m.14766C>T	50023	76.7%	99.9%	96.8%	66.6%	Yes
A	73	G	m.73A>G	49656	76.1%	86.6%	99.0%	67.2%	Yes
A	10398	G	m.10398A>G	28146	43.1%	96.1%	99.6%	16.9%	Yes
C	12705	T	m.12705C>T	26330	40.3%	99.6%	99.3%	12.3%	Yes
C	16223	T	m.16223C>T	24973	38.3%	92.9%	94.0%	12.0%	Yes
A	8701	G	m.8701A>G	21002	32.2%	99.4%	99.2%	0.4%	Yes
T	9540	C	m.9540T>C	20982	32.2%	99.8%	99.7%	0.1%	Yes
T	10873	C	m.10873T>C	20967	32.1%	99.7%	99.4%	0.2%	Yes
G	15301	A	m.15301G>A	18375	28.2%	61.2%	99.6%	0.5%	No
T	489	C	m.489T>C	16738	25.6%	0.1%	98.6%	7.1%	No
G	15043	A	m.15043G>A	15281	23.4%	1.7%	99.6%	3.2%	No
C	10400	T	m.10400C>T	13774	21.1%	0.1%	99.8%	0.0%	No
T	14783	C	m.14783T>C	13773	21.1%	0.0%	99.6%	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	40302	61.8%	63.6%	54.3%	63.8%	Yes
T	310	C	m.310T>C	25373	38.9%	35.2%	39.9%	39.2%	No
C	315	CC	m.315_316insC	19432	29.8%	38.5%	28.3%	28.8%	No
T	152	C	m.152T>C	16627	25.5%	63.2%	20.7%	20.8%	Yes
C	309	CCT	m.309_310insCT	16298	25.0%	18.3%	28.8%	24.9%	No
T	16189	C	m.16189T>C	16039	24.6%	51.2%	14.4%	23.4%	Yes
CA	522	d	m.522_523delCA	14472	22.2%	48.7%	22.7%	17.7%	No
T	16311	C	m.16311T>C	12816	19.6%	52.1%	19.9%	14.3%	Yes
T	146	C	m.146T>C	12693	19.4%	37.4%	18.7%	16.8%	Yes
T	195	C	m.195T>C	12461	19.1%	56.1%	14.9%	14.4%	Yes
T	16362	C	m.16362T>C	10891	16.7%	11.2%	40.0%	10.3%	No
C	16278	T	m.16278C>T	6491	9.9%	51.5%	6.0%	4.4%	Yes
G	1018	A	m.1018G>A	4731	7.2%	64.3%	0.4%	0.1%	Yes
G	7521	A	m.7521G>A	4729	7.2%	62.3%	0.5%	0.4%	Yes
G	769	A	m.769G>A	4690	7.2%	64.5%	0.0%	0.1%	Yes
C	7256	T	m.7256C>T	4525	6.9%	62.4%	0.2%	0.0%	Yes
C	13650	T	m.13650C>T	4518	6.9%	62.2%	0.1%	0.0%	Yes
C	3594	T	m.3594C>T	4503	6.9%	62.4%	0.0%	0.0%	Yes
A	4104	G	m.4104A>G	4481	6.9%	62.0%	0.0%	0.0%	Yes
A	13105	G	m.13105A>G	4368	6.7%	53.1%	1.2%	0.8%	Yes

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† 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.