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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	60394	98.8%	99.2%	99.1%	98.7%	Yes
A	15326	G	m.15326A>G	60299	98.7%	99.6%	98.7%	98.5%	Yes
A	750	G	m.750A>G	60110	98.3%	95.3%	99.7%	98.4%	Yes
A	4769	G	m.4769A>G	59837	97.9%	99.1%	99.6%	97.2%	Yes
A	263	G	m.263A>G	58480	95.7%	83.2%	98.3%	96.9%	Yes
A	1438	G	m.1438A>G	58266	95.3%	82.1%	96.6%	97.1%	Yes
C	7028	T	m.7028C>T	48576	79.5%	99.8%	99.7%	70.2%	Yes
A	2706	G	m.2706A>G	47640	77.9%	91.9%	97.3%	70.0%	Yes
G	11719	A	m.11719G>A	46521	76.1%	99.8%	99.7%	65.3%	Yes
C	14766	T	m.14766C>T	46208	75.6%	99.8%	96.4%	65.6%	Yes
A	73	G	m.73A>G	45908	75.1%	86.3%	98.7%	66.3%	Yes
A	10398	G	m.10398A>G	25902	42.4%	95.7%	99.4%	17.0%	Yes
C	12705	T	m.12705C>T	24217	39.6%	99.5%	99.1%	12.4%	Yes
C	16223	T	m.16223C>T	23047	37.7%	92.5%	94.6%	12.1%	Yes
A	8701	G	m.8701A>G	19124	31.3%	99.3%	99.1%	0.4%	Yes
T	9540	C	m.9540T>C	19089	31.2%	99.8%	99.5%	0.1%	Yes
T	10873	C	m.10873T>C	19075	31.2%	99.7%	99.2%	0.2%	Yes
G	15301	A	m.15301G>A	16588	27.1%	59.8%	99.3%	0.5%	No
T	489	C	m.489T>C	15321	25.1%	0.1%	98.3%	7.3%	No
G	15043	A	m.15043G>A	13873	22.7%	1.8%	99.4%	3.3%	No
C	10400	T	m.10400C>T	12419	20.3%	0.1%	99.6%	0.0%	No
T	14783	C	m.14783T>C	12413	20.3%	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	38046	62.2%	64.0%	54.7%	64.2%	Yes
T	310	C	m.310T>C	24473	40.0%	34.7%	42.6%	40.1%	No
C	315	CC	m.315_316insC	18470	30.2%	38.7%	28.8%	29.3%	No
C	309	CCT	m.309_310insCT	15872	26.0%	17.9%	31.2%	25.7%	No
T	152	C	m.152T>C	15531	25.4%	63.2%	20.8%	20.8%	Yes
T	16189	C	m.16189T>C	14995	24.5%	51.8%	14.5%	23.2%	Yes
CA	522	d	m.522_523delCA	13751	22.5%	50.1%	23.9%	17.7%	No
T	16311	C	m.16311T>C	11703	19.1%	52.4%	17.4%	14.4%	Yes
T	195	C	m.195T>C	11580	18.9%	56.2%	14.4%	14.4%	Yes
T	146	C	m.146T>C	11524	18.9%	37.5%	17.4%	16.3%	Yes
T	16362	C	m.16362T>C	10234	16.7%	10.8%	41.3%	10.4%	No
C	16278	T	m.16278C>T	5999	9.8%	51.1%	6.0%	4.4%	Yes
G	7521	A	m.7521G>A	4419	7.2%	62.8%	0.5%	0.4%	Yes
G	1018	A	m.1018G>A	4409	7.2%	64.6%	0.4%	0.1%	Yes
G	769	A	m.769G>A	4368	7.1%	64.8%	0.0%	0.1%	Yes
C	7256	T	m.7256C>T	4228	6.9%	62.9%	0.2%	0.0%	Yes
C	13650	T	m.13650C>T	4218	6.9%	62.7%	0.1%	0.1%	Yes
C	3594	T	m.3594C>T	4205	6.9%	62.8%	0.0%	0.0%	Yes
A	4104	G	m.4104A>G	4183	6.8%	62.5%	0.0%	0.0%	Yes
A	13105	G	m.13105A>G	4105	6.7%	54.4%	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.