Investment Securities

Investment securities, at fair value, consisted of the following at September 30, 2012 and December 31, 2011.



(In thousands)	Sept. 30, 2012		Dec. 31, 2011
Available for sale	$	9,020,951	$	9,224,702
Trading	13,595		17,853
Non-marketable	117,540		115,832
Total investment securities	$	9,152,086	$	9,358,387

Most of the Company’s investment securities are classified as available for sale, and this portfolio is discussed in more detail below. Securities which are classified as non-marketable include Federal Home Loan Bank (FHLB) stock and Federal Reserve Bank stock held for debt and regulatory purposes, which totaled $45.4 million at September 30, 2012 and $45.3 million at December 31, 2011. Investment in Federal Reserve Bank stock is based on the capital structure of the investing bank, and investment in FHLB stock is tied to the level of borrowings from the FHLB. Non-marketable securities also include private equity investments, which amounted to $72.1 million and $70.5 million at September 30, 2012 and December 31, 2011, respectively.

A summary of the available for sale investment securities by maturity groupings as of September 30, 2012 is shown below. The investment portfolio includes agency mortgage-backed securities, which are guaranteed by agencies such as the FHLMC, FNMA, GNMA and FDIC, in addition to non-agency mortgage-backed securities, which have no guarantee. Also included are certain other asset-backed securities, which are primarily collateralized by credit cards, automobiles, student loans, and commercial loans. These securities differ from traditional debt securities primarily in that they may have uncertain maturity dates and are priced based on estimated prepayment rates on the underlying collateral. The Company does not have exposure to subprime originated mortgage-backed or collateralized debt obligation instruments.



(In thousands)	Amortized Cost		Fair Value
U.S. government and federal agency obligations:
Within 1 year	$	500	$	500
After 1 but within 5 years	217,296		241,881
After 5 but within 10 years	106,679		125,116
Total U.S. government and federal agency obligations	324,475		367,497
Government-sponsored enterprise obligations:
After 1 but within 5 years	108,506		112,286
After 5 but within 10 years	74,682		75,436
After 10 years	191,337		192,468
Total government-sponsored enterprise obligations	374,525		380,190
State and municipal obligations:
Within 1 year	92,856		93,592
After 1 but within 5 years	629,641		655,509
After 5 but within 10 years	510,060		528,245
After 10 years	193,502		183,905
Total state and municipal obligations	1,426,059		1,461,251
Mortgage and asset-backed securities:
Agency mortgage-backed securities	3,311,100		3,471,262
Non-agency mortgage-backed securities	241,657		255,172
Asset-backed securities	2,917,206		2,930,810
Total mortgage and asset-backed securities	6,469,963		6,657,244
Other debt securities:
Within 1 year	45,809		46,574
After 1 but within 5 years	60,744		63,898
After 5 but within 10 years	3,969		4,047
After 10 years	6,988		7,104
Total other debt securities	117,510		121,623
Equity securities	8,483		33,146
Total available for sale investment securities	$	8,721,015	$	9,020,951

Included in U.S. government securities are $366.9 million, at fair value, of U.S. Treasury inflation-protected securities (TIPS). Interest paid on these securities increases with inflation and decreases with deflation, as measured by the Consumer Price Index. Included in state and municipal obligations are $127.7 million, at fair value, of auction rate securities, which were purchased from bank customers in 2008. Included in equity securities is common stock held by the holding company, Commerce Bancshares, Inc. (the Parent), with a fair value of $28.0 million at September 30, 2012.

For securities classified as available for sale, the following table shows the unrealized gains and losses (pre-tax) in accumulated other comprehensive income, by security type.



(In thousands)	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
September 30, 2012
U.S. government and federal agency obligations	$	324,475	$	43,022	$	—		$	367,497
Government-sponsored enterprise obligations	374,525		5,678		(13		)	380,190
State and municipal obligations	1,426,059		48,313		(13,121		)	1,461,251
Mortgage and asset-backed securities:
Agency mortgage-backed securities	3,311,100		160,215		(53		)	3,471,262
Non-agency mortgage-backed securities	241,657		13,698		(183		)	255,172
Asset-backed securities	2,917,206		14,840		(1,236		)	2,930,810
Total mortgage and asset-backed securities	6,469,963		188,753		(1,472		)	6,657,244
Other debt securities	117,510		4,113		—			121,623
Equity securities	8,483		24,663		—			33,146
Total	$	8,721,015	$	314,542	$	(14,606	)	$	9,020,951
December 31, 2011
U.S. government and federal agency obligations	$	328,530	$	36,135	$	—		$	364,665
Government-sponsored enterprise obligations	311,529		4,169		—			315,698
State and municipal obligations	1,220,840		35,663		(11,219		)	1,245,284
Mortgage and asset-backed securities:
Agency mortgage-backed securities	3,989,464		117,088		(493		)	4,106,059
Non-agency mortgage-backed securities	315,752		8,962		(7,812		)	316,902
Asset-backed securities	2,692,436		7,083		(6,376		)	2,693,143
Total mortgage and asset-backed securities	6,997,652		133,133		(14,681		)	7,116,104
Other debt securities	135,190		6,070		—			141,260
Equity securities	18,354		23,337		—			41,691
Total	$	9,012,095	$	238,507	$	(25,900	)	$	9,224,702

The Company’s impairment policy requires a review of all securities for which fair value is less than amortized cost. Special emphasis and analysis is placed on securities whose credit rating has fallen below A3/A-, whose fair values have fallen more than 20% below purchase price for an extended period of time, or have been identified based on management’s judgment. These securities are placed on a watch list, and for all such securities, detailed cash flow models are prepared which use inputs specific to each security. Inputs to these models include factors such as cash flow received, contractual payments required, and various other information related to the underlying collateral (including current delinquencies), collateral loss severity rates (including loan to values), expected delinquency rates, credit support from other tranches, and prepayment speeds. Stress tests are performed at varying levels of delinquency rates, prepayment speeds and loss severities in order to gauge probable ranges of credit loss. At September 30, 2012, the fair value of securities on this watch list was $207.1 million.

As of September 30, 2012, the Company had recorded other-than-temporary impairment (OTTI) on certain non-agency mortgage-backed securities, part of the watch list mentioned above, which had an aggregate fair value of $108.1 million. The credit-related portion of the impairment totaled $11.3 million and was recorded in earnings. The Company does not intend to sell these securities and believes it is not likely that it will be required to sell the securities before the recovery of their amortized cost bases.

The credit portion of the loss on these securities was based on the cash flows projected to be received over the estimated life of the securities, discounted to present value, and compared to the current amortized cost bases of the securities. Significant inputs to the cash flow models used to calculate the credit losses on these securities included the following:



Significant Inputs	Range
Prepayment CPR	0%	-	25%
Projected cumulative default	13%	-	58%
Credit support	0%	-	16%
Loss severity	33%	-	70%

The following table shows changes in the credit losses recorded in the nine months ended September 30, 2012 and 2011, for which a portion of an OTTI was recognized in other comprehensive income.



	For the Nine Months Ended September 30
(In thousands)	2012			2011
Balance at January 1	$	9,931		$	7,542
Credit losses on debt securities for which impairment was not previously recognized	—			53
Credit losses on debt securities for which impairment was previously recognized	1,227			1,702
Increase in expected cash flows that are recognized over remaining life of security	(93		)	(105		)
Balance at September 30	$	11,065		$	9,192

Securities with unrealized losses recorded in accumulated other comprehensive income are shown in the table below, along with the length of the impairment period.



	Less than 12 months				12 months or longer				Total
(In thousands)	Fair Value		Unrealized Losses		Fair Value		Unrealized Losses		Fair Value		Unrealized Losses
September 30, 2012
Government-sponsored enterprise obligations	$	9,979	$	13	$	—	$	—	$	9,979	$	13
State and municipal obligations	16,548		34		98,242		13,087		114,790		13,121
Mortgage and asset-backed securities:
Agency mortgage-backed securities	6,072		5		19,145		48		25,217		53
Non-agency mortgage-backed securities	—		—		19,445		183		19,445		183
Asset-backed securities	122,645		770		90,503		466		213,148		1,236
Total mortgage and asset-backed securities	128,717		775		129,093		697		257,810		1,472
Total	$	155,244	$	822	$	227,335	$	13,784	$	382,579	$	14,606
December 31, 2011
State and municipal obligations	$	65,962	$	712	$	110,807	$	10,507	$	176,769	$	11,219
Mortgage and asset-backed securities:
Agency mortgage-backed securities	72,019		493		—		—		72,019		493
Non-agency mortgage-backed securities	23,672		784		118,972		7,028		142,644		7,812
Asset-backed securities	1,236,526		4,982		87,224		1,394		1,323,750		6,376
Total mortgage and asset-backed securities	1,332,217		6,259		206,196		8,422		1,538,413		14,681
Total	$	1,398,179	$	6,971	$	317,003	$	18,929	$	1,715,182	$	25,900

The total available for sale portfolio consisted of approximately 1,600 individual securities at September 30, 2012. The portfolio included 58 securities, having an aggregate fair value of $382.6 million, that were in a loss position at September 30, 2012. Securities in a loss position for 12 months or longer included those with temporary impairment totaling $215.1 million, or 2.4% of the total portfolio value and other securities identified as other-than-temporarily impaired totaling $12.2 million.

The Company’s holdings of state and municipal obligations included gross unrealized losses of $13.1 million at September 30, 2012. Nearly all of these losses related to auction rate securities (ARS). This portfolio, exclusive of ARS, totaled $1.3 billion at fair value, or 14.8% of total available for sale securities. The average credit quality of the portfolio, excluding ARS, is Aa2 as rated by Moody’s. The portfolio is diversified in order to reduce risk, and information about the top five largest holdings, by state and economic sector, is shown in the table below.



	% of Portfolio		Average Life (in years)	Average Rating (Moody’s)
At September 30, 2012
Texas	9.9	%	5.2	Aa1
Florida	9.5		4.7	Aa2
Washington	6.4		4.2	Aa2
Ohio	5.5		5.3	Aa2
Arizona	4.7		3.4	Aa3
General Obligation	31.8	%	4.8	Aa2
Housing	20.0		6.9	Aa1
Transportation	12.8		3.7	Aa3
Lease	11.8		3.4	Aa3
Limited Tax	7.5		5.6	Aa1

The following table presents proceeds from sales of securities and the components of investment securities gains and losses which have been recognized in earnings.



	For the Nine Months Ended September 30
(In thousands)	2012			2011
Proceeds from sales of available for sale securities	$	4,951		$	11,202
Proceeds from sales of non-marketable securities	9,980			497
Total proceeds	$	14,931		$	11,699
Available for sale:
Gains realized on sales	$	342		$	177
Other-than-temporary impairment recognized on debt securities	(1,227		)	(1,755		)
Non-marketable:
Gains realized on sales	1,267			497
Losses realized on sales	(200		)	—
Fair value adjustments, net	8,374			6,951
Investment securities gains, net	$	8,556		$	5,870

At September 30, 2012, securities carried at $4.0 billion were pledged to secure public fund deposits, securities sold under agreements to repurchase, trust funds, and borrowings at the Federal Reserve Bank and FHLB. Securities pledged under agreements pursuant to which the collateral may be sold or re-pledged by the secured parties approximated $742.1 million, while the remaining securities were pledged under agreements pursuant to which the secured parties may not sell or re-pledge the collateral. Except for obligations of various government-sponsored enterprises such as FNMA, FHLB and FHLMC, no investment in a single issuer exceeded 10% of stockholders’ equity.