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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	15326	G	m.15326A>G	60315	98.6%	99.6%	98.7%	98.4%	Yes
A	8860	G	m.8860A>G	60264	98.5%	99.0%	98.8%	98.4%	Yes
A	750	G	m.750A>G	60122	98.3%	95.2%	99.6%	98.4%	Yes
A	4769	G	m.4769A>G	59732	97.7%	99.1%	99.4%	96.9%	Yes
A	263	G	m.263A>G	58432	95.5%	83.2%	98.2%	96.7%	Yes
A	1438	G	m.1438A>G	58231	95.2%	82.0%	96.4%	96.9%	Yes
C	7028	T	m.7028C>T	48522	79.3%	99.7%	99.6%	70.1%	Yes
A	2706	G	m.2706A>G	47574	77.8%	91.5%	97.2%	69.9%	Yes
G	11719	A	m.11719G>A	46499	76.0%	99.7%	99.6%	65.3%	Yes
C	14766	T	m.14766C>T	46188	75.5%	99.7%	96.3%	65.5%	Yes
A	73	G	m.73A>G	45883	75.0%	86.1%	98.7%	66.3%	Yes
A	10398	G	m.10398A>G	25866	42.3%	95.7%	99.4%	16.9%	Yes
C	12705	T	m.12705C>T	24187	39.5%	99.5%	99.0%	12.4%	Yes
C	16223	T	m.16223C>T	23015	37.6%	92.5%	94.5%	12.1%	Yes
A	8701	G	m.8701A>G	19100	31.2%	99.3%	99.0%	0.4%	Yes
T	9540	C	m.9540T>C	19059	31.2%	99.7%	99.4%	0.1%	Yes
T	10873	C	m.10873T>C	19056	31.2%	99.6%	99.1%	0.2%	Yes
G	15301	A	m.15301G>A	16549	27.1%	59.7%	99.3%	0.5%	No
T	489	C	m.489T>C	15261	24.9%	0.1%	98.3%	7.3%	No
G	15043	A	m.15043G>A	13811	22.6%	1.7%	99.3%	3.3%	No
C	10400	T	m.10400C>T	12357	20.2%	0.1%	99.5%	0.0%	No
T	14783	C	m.14783T>C	12349	20.2%	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	38030	62.2%	64.0%	54.3%	64.2%	Yes
T	310	C	m.310T>C	24266	39.7%	34.5%	42.5%	39.6%	No
C	315	CC	m.315_316insC	18403	30.1%	38.5%	28.4%	29.3%	No
C	309	CCT	m.309_310insCT	15776	25.8%	17.8%	30.9%	25.6%	No
T	152	C	m.152T>C	15550	25.4%	63.1%	20.8%	20.8%	Yes
T	16189	C	m.16189T>C	14962	24.5%	51.8%	14.3%	23.1%	Yes
CA	522	d	m.522_523delCA	13737	22.5%	49.9%	24.0%	17.6%	No
T	16311	C	m.16311T>C	11725	19.2%	52.4%	17.5%	14.4%	Yes
T	195	C	m.195T>C	11562	18.9%	56.1%	14.4%	14.3%	Yes
T	146	C	m.146T>C	11525	18.8%	37.4%	17.5%	16.3%	Yes
T	16362	C	m.16362T>C	10255	16.8%	10.8%	41.6%	10.4%	No
C	16278	T	m.16278C>T	6016	9.8%	51.0%	6.0%	4.4%	Yes
G	7521	A	m.7521G>A	4435	7.3%	62.7%	0.5%	0.4%	Yes
G	1018	A	m.1018G>A	4435	7.3%	64.6%	0.4%	0.1%	Yes
G	769	A	m.769G>A	4394	7.2%	64.7%	0.0%	0.1%	Yes
C	7256	T	m.7256C>T	4253	7.0%	62.8%	0.2%	0.0%	Yes
C	13650	T	m.13650C>T	4243	6.9%	62.6%	0.1%	0.0%	Yes
C	3594	T	m.3594C>T	4227	6.9%	62.8%	0.0%	0.0%	Yes
A	4104	G	m.4104A>G	4207	6.9%	62.5%	0.0%	0.0%	Yes
A	13105	G	m.13105A>G	4134	6.8%	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.

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