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Report date: 2023-06-15

Top Level Haplogroup Markers

All markers shown, except those in parentheses, are present at ≥80% in the top level haplogroups of the current Mitomap dataset. Parentheses indicate variants which are ≥50% but <80%. Lowercase letters indicate transversions (e.g., 3516a). Markers matching the rCRS reference value are indicated with "=" (e.g., 263A=); while these latter markers are important to delineate the haplogroup in the phylogenetic tree, they will not usually be listed in genetic test reports because they are identical to the reference rCRS sequence. There are twelve high frequency ancestral variants in this table that are extremely common across all lineages and, as such, are not generally informative for haplotyping. Conversely, the lack of one or more of these variants may be more of use. These variants are 73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G, & 16519C. For lineage distribution, see https://www.mitomap.org/MITOMAP/TopVariants.

For clinicians and researchers assessing variant pathogenicity: all Ancestral Markers on this page satisfy ClinGen’s BA1 (benign standalone) frequency criteria for mtDNA variants. All haplogroup (HG) markers shown on this page qualify at BA1 for a patient who is a member of the same haplogroup. For a full list of variants satisfying BA1 or BS1 (benign supporting) on a global frequency level, see ClinGenApproved.

For markers found at the letter-number-letter haplogroup level click here.

Lineage	Top Level Haplogroup	# Seqs	Ancestral Marker Motif † (the " RSRS50")	HG Markers	Other Selected Markers
L	L0	1697	247A, 750G, 769A, 825A, 1018A, 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, 16187T, 16189C, 16223T, 16230G, 16311C (73G, 146C, 152C, 195C, 1438G, 2706G, 16129A, 16519C)	1048T, 3516a, 5442C, 6185C, 9042T, 9347G, 9755A, 10589A, 12007A, 12720G (522d, 4586C, 9818T, 16172C)	(263A=)
L	L1	949	73G, 152C, 247A, 263G, 750G, 769A, 825A, 1018A, 2706G, 2758A, 2885C, 3594T, 4104G, 4769G, 7028T, 7146G, 7256T, 7521A, 8468T, 8655T, 8701G, 8860G, 9540C, 10398G, 10688A, 10810C, 10873C, 11719A, 12705T, 13105G, 13506T, 13650T, 14766T, 15326G, 16187T, 16189C, 16223T, 16278T, 16311C, 16519C (195C, 1438G, 16129A)	182T, 3666A, 7055G, 7389C, 13789C, 14178C, 14560A (151T, 186a, 189c, 316A, 522d, 2395d, 5951G, 6071C, 8027A, 9072G, 10586A, 12810G, 13485G, 14000A, 14911T, 16294T, 16360T)
L	L2	1468	73G, 146C, 152C, 195C, 263G, 750G, 769A, 1018A, 1438G, 2706G, 3594T, 4104G, 4769G, 7028T, 7256T, 7521A, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 13650T, 14766T, 15326G, 16223T, 16278T (11914A)	2416C, 8206A, 9221G, 10115C, 11944C, 13590A, 15301A, 16390A (2789T, 7175C, 7274T, 7771G, 12693G, 13803G, 14566G, 15784C, 16294T, 16309G)	150C=, 16311T=
L	L3	2320	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T (16519C)	15301A (150T)	3594C=, 769G=, 1018G=, 16311T=
L	L4	112	73G, 263G, 750G, 769A, 1018A, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T, 16311C (146C, 16519C)	3918A, 15301A, 16362C (244G, 315CC, 1413C, 8104C, 9855G, 12609C, 13470G, 16293T, 16355T, 16399G)	3594C=, L4b2: 146C
L	L5	38	73G, 247A, 263G, 750G, 769A, 825A, 1018A, 1438G, 2706G, 3594T, 4104G, 4769G, 7028T, 7256T, 7521A, 8655T, 8701G, 8860G, 9540C, 10398G, 10688A, 10810C, 10873C, 11719A, 12705T, 13506T, 13650T, 14766T, 15326G, 16129A, 16223T, 16278T, 16311C (152C, 195C, 13105G, 16189C)	182T, 3423C, 5147A, 7972G, 12432T, 12950G, 14581C, 16148T, 16166G (522d, 709A, 851G, 1822C, 5111T, 5656G, 6182A, 6297C, 7424G, 8155A, 8188G, 8582T, 9305A, 9329A, 11025C, 11881T, 12236A, 13722G, 14212C, 14239T, 14905A, 14971C, 15217A, 15884A, 16355T, 16362C)	Length variants in the 455-459 region [459CCsor 455TTC or 455TTTC].
L	L6	12	73G, 146C, 152C, 263G, 750G, 769A, 1018A, 1438G, 2706G, 3594T, 4769G, 7028T, 7256T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 13650T, 14766T, 15326G, 16223T, 16278T, 16311C, 16519C	182T, 185C, 709A, 770T, 961C, 1461G, 4964T, 5267C, 6002G, 6284G, 9332T, 10978G, 11116C, 11743T, 12771A, 13710G, 14791T, 14959G, 15244G, 15289C, 15301A, 15499T, 16048A, 16224C (265C, 309CCT, 310C)
M	C	2093	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 11914A, 12705T, 14766T, 15326G, 16223T (16519C)	249d, 489C, 3552A, 4715G, 7196a, 8584A, 9545G, 10400T, 13263G, 14318C, 14783C, 15043A, 15301A, 15487T, 16298C, 16327T
M	D	2738	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T	489C, 3010A, 4883T, 5178a, 8414T, 10400T, 14668T, 14783C, 15043A, 15301A, 16362C
M	E	474	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 15326G, 16223T, 16519C	489C, 3027C, 3705A, 4248C, 4491A, 7598A, 10400T, 10834T, 13254C, 13626T, 14577C, 14783C, 15043A, 15301A, 16362C, 16390A (6620C, 16291T)
M	G	585	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T	489C, 709A, 4833G, 5108C, 10400T, 14569A, 14783C, 15043A, 15301A, 16362C (5601T, 13563G)
M	M	5602	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16223T (16519C)	489C, 10400T, 14783C, 15043A, 15301A
M	Q	424	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 15326G, 16129A, 16311C (146C, 16223T)	89C, 489C, 4117C, 5460A, 5843G, 8790A, 8964T, 10400T, 12940A, 13500C, 14025C, 14783C, 15043A, 15301A, 16144C, 16148T, 16241G, 16265c (92A, 16343G)
M	Z	269	73G, 152C, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8701G, 8860G, 9540C, 10398G, 10873C, 11719A, 12705T, 14766T, 16223T (15326G)	249d, 489C, 4715G, 6752G, 7196a, 8584A, 9090C, 10400T, 14783C, 15043A, 15301A, 15487T, 15784C, 16185T, 16260T, 16298C (310C)
N	A	1721	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T (146C)	235G, 522d, 663G, 1736G, 4248C, 4824G, 8794T, 16290T, 16319A, 16362C (153G, 310C, 8027A, 12007A, 16111T)
N	B	4878	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G, 16189C, 16519C (146C)	16183c, 16217C	Branches B4 and B9: 10398A=,s8271 9bp deletions [8271_8279del or 8281_8289del]; Branch B4: 514_515delCA Branch B5: 146T=, 16217T=
N	F	1907	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G (16129A, 16519C)	3970T, 6392C, 10310A, 13928C, 16304C (249d, 522d, 6962A, 9053A, 10609C, 12406A, 12882T, 13759A)
N	H	12052	263G, 750G, 1438G, 4769G, 8860G, 15326G (16519C)		2706A=, 7028C=
N	HV	921	263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 15326G	(310C)	14766C=
N	I	917	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 12705T, 14766T, 15326G, 16129A, 16223T, 16519C	199C, 204C, 250C, 1719A, 4529T, 8251A, 10034C, 10238C, 12501A, 13780G, 15043A, 15924G, 16391A
N	J	2930	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 14766T, 15326G	295T, 489C, 4216C, 11251G, 12612G, 13708A, 15452a, 16069T, 16126C (462T, 3010A, 14798C)
N	K	2183	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 14766T, 15326G, 16311C, 16519C	1189C, 1811G, 3480G, 9055A, 9698C, 10550G, 11299C, 11467G, 12308G, 12372A, 14167T, 14798C, 16224C (315CC, 497T)
N	N	914	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T (16519C)		8701A=, 9540T=, 10398A=, 10400C=, 10873T=, 15301G=
N	O	8	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T (152C, 16189C, 16519C)	6755A, 9140T, 16213A (794C, 5563A, 16183c)
N	P	414	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G	15607G
N	R	1204	263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 14766T, 15326G (73G, 11719A, 16519C)		12705C=, 16223C=
N	S	49	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G (152C, 16223T)	8404C
N	T	2808	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G, 16519C	709A, 1888A, 4216C, 4917G, 8697A, 10463C, 11251G, 13368A, 14905A, 15452a, 15607G, 15928A, 16126C, 16294T (11812G, 14233G)	10398A=
N	U	5334	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G	11467G, 12308G, 12372A
N	V	860	263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 15326G	72C, 4580A, 15904T, 16298C (310C)
N	W	645	73G, 195C, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16223T, 16519C	189G, 204C, 207A, 709A, 1243C, 3505G, 5046A, 5460A, 8251A, 8994A, 11674T, 11947G, 12414C, 15884C, 16292T (194T)
N	X	661	73G, 195C, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 11719A, 12705T, 14766T, 15326G, 16189C, 16223T, 16278T, 16519C	153G, 1719A, 6221C, 6371T, 13966G, 14470C (225A)
N	Y	202	73G, 263G, 750G, 1438G, 2706G, 4769G, 7028T, 8860G, 10398G, 11719A, 12705T, 14766T, 15326G (146C, 16519C)	5417A, 8392A, 14178C, 14693G, 16126C, 16231C (310C, 3834A, 7933G, 16266T)	16223C=

† 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. 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.