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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	58551	98.6%	99.5%	98.7%	98.4%	Yes
A	8860	G	m.8860A>G	58492	98.5%	99.0%	98.8%	98.3%	Yes
A	750	G	m.750A>G	58362	98.3%	95.3%	99.7%	98.3%	Yes
A	4769	G	m.4769A>G	57976	97.6%	99.0%	99.4%	96.8%	Yes
A	263	G	m.263A>G	56674	95.4%	82.9%	98.2%	96.6%	Yes
A	1438	G	m.1438A>G	56493	95.1%	82.0%	96.4%	96.9%	Yes
C	7028	T	m.7028C>T	47185	79.5%	99.7%	99.6%	70.1%	Yes
A	2706	G	m.2706A>G	46247	77.9%	91.4%	97.2%	69.9%	Yes
G	11719	A	m.11719G>A	45227	76.2%	99.7%	99.6%	65.3%	Yes
C	14766	T	m.14766C>T	44918	75.6%	99.7%	96.2%	65.5%	Yes
A	73	G	m.73A>G	44589	75.1%	85.9%	98.7%	66.2%	Yes
A	10398	G	m.10398A>G	25276	42.6%	95.6%	99.4%	16.9%	Yes
C	12705	T	m.12705C>T	23743	40.0%	99.5%	99.1%	12.6%	Yes
C	16223	T	m.16223C>T	22583	38.0%	92.4%	94.5%	12.2%	Yes
A	8701	G	m.8701A>G	18737	31.5%	99.3%	99.0%	0.3%	Yes
T	9540	C	m.9540T>C	18724	31.5%	99.7%	99.4%	0.1%	Yes
T	10873	C	m.10873T>C	18714	31.5%	99.6%	99.2%	0.1%	Yes
G	15301	A	m.15301G>A	16237	27.3%	59.3%	99.3%	0.5%	No
T	489	C	m.489T>C	14914	25.1%	0.1%	98.4%	7.2%	No
G	15043	A	m.15043G>A	13544	22.8%	1.7%	99.3%	3.3%	No
C	10400	T	m.10400C>T	12140	20.4%	0.1%	99.5%	0.0%	No
T	14783	C	m.14783T>C	12131	20.4%	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	36914	62.2%	64.3%	54.3%	64.2%	Yes
T	310	C	m.310T>C	23892	40.2%	34.9%	42.7%	40.4%	No
C	315	CC	m.315_316insC	18151	30.6%	39.1%	28.3%	29.9%	No
C	309	CCT	m.309_310insCT	15611	26.3%	18.1%	31.3%	26.1%	No
T	152	C	m.152T>C	15140	25.5%	63.3%	20.7%	20.8%	Yes
T	16189	C	m.16189T>C	14736	24.8%	52.4%	14.4%	23.5%	Yes
CA	522	d	m.522_523delCA	13414	22.6%	49.8%	24.3%	17.7%	No
T	146	C	m.146T>C	11290	19.0%	37.4%	17.5%	16.5%	Yes
T	16311	C	m.16311T>C	11290	19.0%	52.6%	17.3%	14.1%	Yes
T	195	C	m.195T>C	11211	18.9%	56.2%	14.3%	14.2%	Yes
T	16362	C	m.16362T>C	10067	17.0%	10.7%	41.8%	10.5%	No
C	16278	T	m.16278C>T	5864	9.9%	50.8%	6.0%	4.4%	Yes
G	1018	A	m.1018G>A	4369	7.4%	64.8%	0.4%	0.1%	Yes
G	7521	A	m.7521G>A	4359	7.3%	62.8%	0.5%	0.4%	Yes
G	769	A	m.769G>A	4328	7.3%	64.9%	0.0%	0.1%	Yes
C	7256	T	m.7256C>T	4185	7.0%	63.0%	0.2%	0.0%	Yes
C	13650	T	m.13650C>T	4175	7.0%	62.8%	0.1%	0.1%	Yes
C	3594	T	m.3594C>T	4161	7.0%	62.9%	0.0%	0.0%	Yes
A	4104	G	m.4104A>G	4142	7.0%	62.6%	0.0%	0.0%	Yes
A	13105	G	m.13105A>G	4076	6.9%	54.7%	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.