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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	61219	99.0%	99.2%	99.3%	98.9%	Yes
A	15326	G	m.15326A>G	61130	98.8%	99.7%	98.9%	98.7%	Yes
A	750	G	m.750A>G	60935	98.5%	95.4%	99.8%	98.6%	Yes
A	4769	G	m.4769A>G	60667	98.1%	99.2%	99.8%	97.4%	Yes
A	263	G	m.263A>G	59299	95.9%	83.3%	98.5%	97.1%	Yes
A	1438	G	m.1438A>G	59088	95.5%	82.2%	96.8%	97.3%	Yes
C	7028	T	m.7028C>T	49382	79.8%	99.8%	99.8%	70.7%	Yes
A	2706	G	m.2706A>G	48426	78.3%	91.9%	97.4%	70.4%	Yes
G	11719	A	m.11719G>A	47324	76.5%	99.8%	99.9%	65.8%	Yes
C	14766	T	m.14766C>T	47013	76.0%	99.9%	96.6%	66.1%	Yes
A	73	G	m.73A>G	46698	75.5%	86.3%	98.9%	66.7%	Yes
A	10398	G	m.10398A>G	26384	42.7%	95.7%	99.6%	17.1%	Yes
C	12705	T	m.12705C>T	24619	39.8%	99.6%	99.3%	12.4%	Yes
C	16223	T	m.16223C>T	23436	37.9%	92.6%	94.8%	12.1%	Yes
A	8701	G	m.8701A>G	19471	31.5%	99.4%	99.1%	0.4%	Yes
T	9540	C	m.9540T>C	19447	31.4%	99.8%	99.7%	0.1%	Yes
T	10873	C	m.10873T>C	19432	31.4%	99.7%	99.4%	0.2%	Yes
G	15301	A	m.15301G>A	16954	27.4%	59.8%	99.5%	0.5%	No
T	489	C	m.489T>C	15676	25.3%	0.1%	98.5%	7.2%	No
G	15043	A	m.15043G>A	14241	23.0%	1.7%	99.5%	3.3%	No
C	10400	T	m.10400C>T	12772	20.7%	0.1%	99.7%	0.0%	No
T	14783	C	m.14783T>C	12770	20.6%	0.0%	99.5%	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	38644	62.5%	64.0%	54.9%	64.6%	Yes
T	310	C	m.310T>C	24726	40.0%	34.7%	42.4%	40.1%	No
C	315	CC	m.315_316insC	18754	30.3%	38.7%	29.2%	29.4%	No
C	309	CCT	m.309_310insCT	16017	25.9%	17.9%	30.9%	25.7%	No
T	152	C	m.152T>C	15684	25.4%	63.2%	20.9%	20.7%	Yes
T	16189	C	m.16189T>C	15259	24.7%	51.8%	14.7%	23.4%	Yes
CA	522	d	m.522_523delCA	14114	22.8%	50.1%	24.1%	18.1%	No
T	16311	C	m.16311T>C	11825	19.1%	52.4%	17.6%	14.3%	Yes
T	146	C	m.146T>C	11691	18.9%	37.5%	17.4%	16.4%	Yes
T	195	C	m.195T>C	11678	18.9%	56.2%	14.5%	14.4%	Yes
T	16362	C	m.16362T>C	10351	16.7%	10.8%	40.9%	10.4%	No
C	16278	T	m.16278C>T	6048	9.8%	51.1%	6.2%	4.4%	Yes
G	7521	A	m.7521G>A	4427	7.2%	62.8%	0.5%	0.4%	Yes
G	1018	A	m.1018G>A	4410	7.1%	64.7%	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	4227	6.8%	62.9%	0.2%	0.0%	Yes
C	13650	T	m.13650C>T	4221	6.8%	62.7%	0.1%	0.0%	Yes
C	3594	T	m.3594C>T	4205	6.8%	62.9%	0.0%	0.0%	Yes
A	4104	G	m.4104A>G	4185	6.8%	62.6%	0.0%	0.0%	Yes
A	13105	G	m.13105A>G	4115	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.